{ "dbId" : 10910990, "stableId" : "R-DME-73933", "displayName" : "Resolution of Abasic Sites (AP sites)", "nodes" : [ { "id" : 5088, "reactomeId" : 10836067, "displayName" : "Tdg", "schemaClass" : "EntityWithAccessionedSequence", "renderableClass" : "Protein", "position" : { "x" : 616, "y" : 425 }, "minX" : 590, "maxX" : 648, "minY" : 408, "maxY" : 456, "prop" : { "x" : 590, "y" : 414, "width" : 52, "height" : 23 }, "textPosition" : { "x" : 600, "y" : 415 }, "interactorsSummary" : { "type" : "TR", "shape" : { "c" : { "x" : 642, "y" : 414 }, "r" : 6, "type" : "CIRCLE", "empty" : true, "centre" : { "x" : 642, "y" : 414 } } }, "connectors" : [ { "edgeId" : 5084, "type" : "OUTPUT", "segments" : [ { "from" : { "x" : 609, "y" : 440 }, "to" : { "x" : 598, "y" : 456 } } ], "stoichiometry" : { "value" : 1 }, "endShape" : { "a" : { "x" : 608, "y" : 448 }, "b" : { "x" : 609, "y" : 440 }, "c" : { "x" : 602, "y" : 443 }, "type" : "ARROW", "centre" : { "x" : 602, "y" : 443 } } } ] }, { "id" : 5090, "reactomeId" : 10836262, "displayName" : "SMUG1:AP-dsDNA", "schemaClass" : "Complex", "renderableClass" : "Complex", "position" : { "x" : 504, "y" : 500 }, "minX" : 444, "maxX" : 570, "minY" : 483, "maxY" : 544, "prop" : { "x" : 444, "y" : 489, "width" : 120, "height" : 22 }, "textPosition" : { "x" : 445, "y" : 490 }, "bgColor" : { "r" : 204, "g" : 255, "b" : 255 }, "interactorsSummary" : { "type" : "TR", "shape" : { "c" : { "x" : 564, "y" : 489 }, "r" : 6, "type" : "CIRCLE", "empty" : true, "centre" : { "x" : 564, "y" : 489 } } }, "connectors" : [ { "edgeId" : 5089, "type" : "INPUT", "segments" : [ { "from" : { "x" : 510, "y" : 514 }, "to" : { "x" : 530, "y" : 544 } } ], "stoichiometry" : { "value" : 1 } } ] }, { "id" : 5091, "reactomeId" : 10836072, "displayName" : "Smug", "schemaClass" : "EntityWithAccessionedSequence", "renderableClass" : "Protein", "position" : { "x" : 649, "y" : 505 }, "minX" : 620, "maxX" : 685, "minY" : 486, "maxY" : 544, "prop" : { "x" : 620, "y" : 492, "width" : 59, "height" : 26 }, "textPosition" : { "x" : 628, "y" : 494 }, "interactorsSummary" : { "type" : "TR", "shape" : { "c" : { "x" : 679, "y" : 492 }, "r" : 6, "type" : "CIRCLE", "empty" : true, "centre" : { "x" : 679, "y" : 492 } } }, "connectors" : [ { "edgeId" : 5089, "type" : "OUTPUT", "segments" : [ { "from" : { "x" : 641, "y" : 521 }, "to" : { "x" : 627, "y" : 544 } } ], "stoichiometry" : { "value" : 1 }, "endShape" : { "a" : { "x" : 641, "y" : 529 }, "b" : { "x" : 641, "y" : 521 }, "c" : { "x" : 634, "y" : 525 }, "type" : "ARROW", "centre" : { "x" : 634, "y" : 525 } } } ] }, { "id" : 5093, "reactomeId" : 10836112, "displayName" : "NTHL1:AP-dsDNA", "schemaClass" : "Complex", "renderableClass" : "Complex", "position" : { "x" : 491, "y" : 578 }, "minX" : 433, "maxX" : 556, "minY" : 559, "maxY" : 619, "prop" : { "x" : 433, "y" : 565, "width" : 117, "height" : 26 }, "textPosition" : { "x" : 435, "y" : 570 }, "bgColor" : { "r" : 204, "g" : 255, "b" : 255 }, "interactorsSummary" : { "type" : "TR", "shape" : { "c" : { "x" : 550, "y" : 565 }, "r" : 6, "type" : "CIRCLE", "empty" : true, "centre" : { "x" : 550, "y" : 565 } } }, "connectors" : [ { "edgeId" : 5092, "type" : "INPUT", "segments" : [ { "from" : { "x" : 496, "y" : 594 }, "to" : { "x" : 508, "y" : 619 } } ], "stoichiometry" : { "value" : 1 } } ] }, { "id" : 5094, "reactomeId" : 10836077, "displayName" : "Nthl1", "schemaClass" : "EntityWithAccessionedSequence", "renderableClass" : "Protein", "position" : { "x" : 678, "y" : 573 }, "minX" : 653, "maxX" : 710, "minY" : 555, "maxY" : 624, "prop" : { "x" : 653, "y" : 561, "width" : 51, "height" : 25 }, "textPosition" : { "x" : 658, "y" : 563 }, "interactorsSummary" : { "type" : "TR", "shape" : { "c" : { "x" : 704, "y" : 561 }, "r" : 6, "type" : "CIRCLE", "empty" : true, "centre" : { "x" : 704, "y" : 561 } } }, "connectors" : [ { "edgeId" : 5092, "type" : "OUTPUT", "segments" : [ { "from" : { "x" : 674, "y" : 589 }, "to" : { "x" : 662, "y" : 624 } } ], "stoichiometry" : { "value" : 1 }, "endShape" : { "a" : { "x" : 676, "y" : 597 }, "b" : { "x" : 674, "y" : 589 }, "c" : { "x" : 668, "y" : 594 }, "type" : "ARROW", "centre" : { "x" : 668, "y" : 594 } } } ] }, { "id" : 5096, "reactomeId" : 10836154, "displayName" : "OGG1:AP-dsDNA", "schemaClass" : "Complex", "renderableClass" : "Complex", "position" : { "x" : 422, "y" : 955 }, "minX" : 363, "maxX" : 487, "minY" : 917, "maxY" : 969, "prop" : { "x" : 363, "y" : 942, "width" : 118, "height" : 27 }, "textPosition" : { "x" : 368, "y" : 948 }, "bgColor" : { "r" : 204, "g" : 255, "b" : 255 }, "interactorsSummary" : { "type" : "TR", "shape" : { "c" : { "x" : 481, "y" : 942 }, "r" : 6, "type" : "CIRCLE", "empty" : true, "centre" : { "x" : 481, "y" : 942 } } }, "connectors" : [ { "edgeId" : 5095, "type" : "INPUT", "segments" : [ { "from" : { "x" : 428, "y" : 939 }, "to" : { "x" : 440, "y" : 917 } } ], "stoichiometry" : { "value" : 1 } } ] }, { "id" : 5097, "reactomeId" : 10836148, "displayName" : "OGG1", "schemaClass" : "EntityWithAccessionedSequence", "renderableClass" : "Protein", "position" : { "x" : 691, "y" : 963 }, "minX" : 660, "maxX" : 728, "minY" : 926, "maxY" : 974, "prop" : { "x" : 660, "y" : 953, "width" : 62, "height" : 21 }, "textPosition" : { "x" : 669, "y" : 953 }, "interactorsSummary" : { "type" : "TR", "shape" : { "c" : { "x" : 722, "y" : 953 }, "r" : 6, "type" : "CIRCLE", "empty" : true, "centre" : { "x" : 722, "y" : 953 } } }, "connectors" : [ { "edgeId" : 5095, "type" : "OUTPUT", "segments" : [ { "from" : { "x" : 683, "y" : 950 }, "to" : { "x" : 663, "y" : 926 } } ], "stoichiometry" : { "value" : 1 }, "endShape" : { "a" : { "x" : 675, "y" : 947 }, "b" : { "x" : 683, "y" : 950 }, "c" : { "x" : 682, "y" : 942 }, "type" : "ARROW", "centre" : { "x" : 682, "y" : 942 } } } ] }, { "id" : 5099, "reactomeId" : 10836272, "displayName" : "APEX1:SSB(AP->5'-dRP)-dsDNA", "schemaClass" : "Complex", "renderableClass" : "Complex", "position" : { "x" : 1134, "y" : 594 }, "minX" : 1028, "maxX" : 1246, "minY" : 576, "maxY" : 606, "prop" : { "x" : 1028, "y" : 582, "width" : 212, "height" : 24 }, "textPosition" : { "x" : 1034, "y" : 585 }, "bgColor" : { "r" : 204, "g" : 255, "b" : 255 }, "interactorsSummary" : { "type" : "TR", "shape" : { "c" : { "x" : 1240, "y" : 582 }, "r" : 6, "type" : "CIRCLE", "empty" : true, "centre" : { "x" : 1240, "y" : 582 } } }, "connectors" : [ { "edgeId" : 5098, "type" : "OUTPUT", "segments" : [ ], "stoichiometry" : { "value" : 1 } }, { "edgeId" : 5100, "type" : "INPUT", "segments" : [ ], "stoichiometry" : { "value" : 1 } } ] }, { "id" : 5101, "reactomeId" : 10879915, "displayName" : "APEX1:SSB(5'-ddRP)-dsDNA", "schemaClass" : "Complex", "renderableClass" : "Complex", "position" : { "x" : 1137, "y" : 709 }, "minX" : 1096, "maxX" : 1184, "minY" : 678, "maxY" : 734, "prop" : { "x" : 1096, "y" : 684, "width" : 82, "height" : 50 }, "textPosition" : { "x" : 1099, "y" : 685 }, "bgColor" : { "r" : 204, "g" : 255, "b" : 255 }, "interactorsSummary" : { "type" : "TR", "shape" : { "c" : { "x" : 1178, "y" : 684 }, "r" : 6, "type" : "CIRCLE", "empty" : true, "centre" : { "x" : 1178, "y" : 684 } } }, "connectors" : [ { "edgeId" : 5100, "type" : "OUTPUT", "segments" : [ ], "stoichiometry" : { "value" : 1 } } ] }, { "id" : 5103, "reactomeId" : 10836287, "displayName" : "APEX1:FEN1:PCNA:POLD,POLE:RPA:RFC:SSB(3'dNMP-displaced 5'ddRP)-dsDNA", "schemaClass" : "Complex", "renderableClass" : "Complex", "position" : { "x" : 1645, "y" : 1114 }, "minX" : 1573, "maxX" : 1827, "minY" : 1076, "maxY" : 1147, "prop" : { "x" : 1573, "y" : 1082, "width" : 144, "height" : 65 }, "textPosition" : { "x" : 1578, "y" : 1070 }, "bgColor" : { "r" : 204, "g" : 255, "b" : 255 }, "interactorsSummary" : { "type" : "TR", "shape" : { "c" : { "x" : 1717, "y" : 1082 }, "r" : 6, "type" : "CIRCLE", "empty" : true, "centre" : { "x" : 1717, "y" : 1082 } } }, "connectors" : [ { "edgeId" : 5102, "type" : "INPUT", "segments" : [ { "from" : { "x" : 1720, "y" : 1111 }, "to" : { "x" : 1779, "y" : 1110 } } ], "stoichiometry" : { "value" : 1 } }, { "edgeId" : 5102, "type" : "CATALYST", "segments" : [ { "from" : { "x" : 1720, "y" : 1134 }, "to" : { "x" : 1763, "y" : 1147 } }, { "from" : { "x" : 1763, "y" : 1147 }, "to" : { "x" : 1819, "y" : 1115 } } ], "stoichiometry" : { "value" : 1 }, "endShape" : { "c" : { "x" : 1823, "y" : 1113 }, "r" : 4, "type" : "CIRCLE", "empty" : true, "centre" : { "x" : 1823, "y" : 1113 } } } ] }, { "id" : 5104, "reactomeId" : 30555, "displayName" : "dNTP", "schemaClass" : "SimpleEntity", "renderableClass" : "Chemical", "position" : { "x" : 1832, "y" : 996 }, "minX" : 1779, "maxX" : 1856, "minY" : 982, "maxY" : 1110, "prop" : { "x" : 1810, "y" : 983, "width" : 45, "height" : 27 }, "textPosition" : { "x" : 1812, "y" : 986 }, "interactorsSummary" : { "type" : "TR", "shape" : { "c" : { "x" : 1850, "y" : 988 }, "r" : 6, "type" : "CIRCLE", "empty" : true, "centre" : { "x" : 1850, "y" : 988 } } }, "connectors" : [ { "edgeId" : 5102, "type" : "INPUT", "segments" : [ { "from" : { "x" : 1825, "y" : 1013 }, "to" : { "x" : 1779, "y" : 1110 } } ], "stoichiometry" : { "value" : 10, "shape" : { "a" : { "x" : 1796, "y" : 1055 }, "b" : { "x" : 1808, "y" : 1067 }, "type" : "BOX", "empty" : true, "centre" : { "x" : 1802, "y" : 1061 } } } } ] }, { "id" : 5105, "reactomeId" : 10836283, "displayName" : "APEX1:FEN1:PCNA:POLD,POLE:RPA:RFC:SSB(3'poly-dNMP-displaced 5'ddRP flap)-dsDNA", "schemaClass" : "Complex", "renderableClass" : "Complex", "position" : { "x" : 2019, "y" : 1101 }, "minX" : 1870, "maxX" : 2122, "minY" : 1068, "maxY" : 1128, "prop" : { "x" : 1922, "y" : 1074, "width" : 194, "height" : 54 }, "textPosition" : { "x" : 1924, "y" : 1065 }, "bgColor" : { "r" : 204, "g" : 255, "b" : 255 }, "interactorsSummary" : { "type" : "TR", "shape" : { "c" : { "x" : 2116, "y" : 1074 }, "r" : 6, "type" : "CIRCLE", "empty" : true, "centre" : { "x" : 2116, "y" : 1074 } } }, "connectors" : [ { "edgeId" : 5102, "type" : "OUTPUT", "segments" : [ { "from" : { "x" : 1919, "y" : 1104 }, "to" : { "x" : 1870, "y" : 1106 } } ], "stoichiometry" : { "value" : 1 }, "endShape" : { "a" : { "x" : 1912, "y" : 1108 }, "b" : { "x" : 1919, "y" : 1104 }, "c" : { "x" : 1912, "y" : 1100 }, "type" : "ARROW", "centre" : { "x" : 1912, "y" : 1100 } } } ] }, { "id" : 5106, "reactomeId" : 113541, "displayName" : "PPi", "schemaClass" : "SimpleEntity", "renderableClass" : "Chemical", "position" : { "x" : 1922, "y" : 996 }, "minX" : 1870, "maxX" : 1950, "minY" : 982, "maxY" : 1106, "prop" : { "x" : 1895, "y" : 983, "width" : 54, "height" : 26 }, "textPosition" : { "x" : 1908, "y" : 985 }, "interactorsSummary" : { "type" : "TR", "shape" : { "c" : { "x" : 1944, "y" : 988 }, "r" : 6, "type" : "CIRCLE", "empty" : true, "centre" : { "x" : 1944, "y" : 988 } } }, "connectors" : [ { "edgeId" : 5102, "type" : "OUTPUT", "segments" : [ { "from" : { "x" : 1915, "y" : 1012 }, "to" : { "x" : 1870, "y" : 1106 } } ], "stoichiometry" : { "value" : 10, "shape" : { "a" : { "x" : 1886, "y" : 1053 }, "b" : { "x" : 1898, "y" : 1065 }, "type" : "BOX", "empty" : true, "centre" : { "x" : 1892, "y" : 1059 } } }, "endShape" : { "a" : { "x" : 1916, "y" : 1020 }, "b" : { "x" : 1915, "y" : 1012 }, "c" : { "x" : 1908, "y" : 1017 }, "type" : "ARROW", "centre" : { "x" : 1908, "y" : 1017 } } } ] }, { "id" : 5108, "reactomeId" : 10836294, "displayName" : "APEX1:PCNA:POLD,POLE:RPA:RFC:SSB(3'poly-dNMP)-dsDNA", "schemaClass" : "Complex", "renderableClass" : "Complex", "position" : { "x" : 2459, "y" : 1117 }, "minX" : 2379, "maxX" : 2545, "minY" : 1084, "maxY" : 1183, "prop" : { "x" : 2379, "y" : 1090, "width" : 160, "height" : 54 }, "textPosition" : { "x" : 2379, "y" : 1095 }, "bgColor" : { "r" : 204, "g" : 255, "b" : 255 }, "interactorsSummary" : { "type" : "TR", "shape" : { "c" : { "x" : 2539, "y" : 1090 }, "r" : 6, "type" : "CIRCLE", "empty" : true, "centre" : { "x" : 2539, "y" : 1090 } } }, "connectors" : [ { "edgeId" : 5107, "type" : "INPUT", "segments" : [ { "from" : { "x" : 2459, "y" : 1147 }, "to" : { "x" : 2460, "y" : 1183 } } ], "stoichiometry" : { "value" : 1 } } ] }, { "id" : 5109, "reactomeId" : 10830148, "displayName" : "DNAlig1", "schemaClass" : "EntityWithAccessionedSequence", "renderableClass" : "Protein", "position" : { "x" : 2613, "y" : 1062 }, "minX" : 2460, "maxX" : 2642, "minY" : 1045, "maxY" : 1183, "prop" : { "x" : 2590, "y" : 1051, "width" : 46, "height" : 23 }, "textPosition" : { "x" : 2593, "y" : 1045 }, "interactorsSummary" : { "type" : "TR", "shape" : { "c" : { "x" : 2636, "y" : 1051 }, "r" : 6, "type" : "CIRCLE", "empty" : true, "centre" : { "x" : 2636, "y" : 1051 } } }, "connectors" : [ { "edgeId" : 5107, "type" : "INPUT", "segments" : [ { "from" : { "x" : 2603, "y" : 1077 }, "to" : { "x" : 2517, "y" : 1181 } }, { "from" : { "x" : 2517, "y" : 1181 }, "to" : { "x" : 2460, "y" : 1183 } } ], "stoichiometry" : { "value" : 1 } } ] }, { "id" : 5110, "reactomeId" : 10836296, "displayName" : "LIG1:APEX1:PCNA:POLD,POLE:RPA:RFC:SSB:(3'poly-dNMP)-dsDNA", "schemaClass" : "Complex", "renderableClass" : "Complex", "position" : { "x" : 2465, "y" : 1243 }, "minX" : 2371, "maxX" : 2565, "minY" : 1209, "maxY" : 1317, "prop" : { "x" : 2371, "y" : 1215, "width" : 188, "height" : 56 }, "textPosition" : { "x" : 2379, "y" : 1222 }, "bgColor" : { "r" : 204, "g" : 255, "b" : 255 }, "interactorsSummary" : { "type" : "TR", "shape" : { "c" : { "x" : 2559, "y" : 1215 }, "r" : 6, "type" : "CIRCLE", "empty" : true, "centre" : { "x" : 2559, "y" : 1215 } } }, "connectors" : [ { "edgeId" : 5107, "type" : "OUTPUT", "segments" : [ ], "stoichiometry" : { "value" : 1 } }, { "edgeId" : 5111, "type" : "INPUT", "segments" : [ ], "stoichiometry" : { "value" : 1 } }, { "edgeId" : 5111, "type" : "CATALYST", "segments" : [ { "from" : { "x" : 2436, "y" : 1274 }, "to" : { "x" : 2413, "y" : 1294 } }, { "from" : { "x" : 2413, "y" : 1294 }, "to" : { "x" : 2455, "y" : 1312 } } ], "stoichiometry" : { "value" : 1 }, "endShape" : { "c" : { "x" : 2459, "y" : 1313 }, "r" : 4, "type" : "CIRCLE", "empty" : true, "centre" : { "x" : 2459, "y" : 1313 } } } ] }, { "id" : 5112, "reactomeId" : 10879943, "displayName" : "LIG1:APEX1:PCNA:POLD,POLE:RPA:RFC:dsDNA", "schemaClass" : "Complex", "renderableClass" : "Complex", "position" : { "x" : 2474, "y" : 1372 }, "minX" : 2379, "maxX" : 2576, "minY" : 1348, "maxY" : 1391, "prop" : { "x" : 2379, "y" : 1354, "width" : 191, "height" : 37 }, "textPosition" : { "x" : 2380, "y" : 1356 }, "bgColor" : { "r" : 204, "g" : 255, "b" : 255 }, "interactorsSummary" : { "type" : "TR", "shape" : { "c" : { "x" : 2570, "y" : 1354 }, "r" : 6, "type" : "CIRCLE", "empty" : true, "centre" : { "x" : 2570, "y" : 1354 } } }, "connectors" : [ { "edgeId" : 5111, "type" : "OUTPUT", "segments" : [ ], "stoichiometry" : { "value" : 1 } } ] }, { "id" : 5116, "reactomeId" : 10910972, "displayName" : "Base-Excision Repair, AP Site Formation", "schemaClass" : "Pathway", "renderableClass" : "EncapsulatedNode", "position" : { "x" : 150, "y" : 665 }, "minX" : 75, "maxX" : 226, "minY" : 621, "maxY" : 709, "prop" : { "x" : 75, "y" : 621, "width" : 151, "height" : 88 }, "textPosition" : { "x" : 74, "y" : 643 }, "connectors" : [ ] }, { "id" : 5085, "reactomeId" : 10836256, "displayName" : "APEX1", "schemaClass" : "EntityWithAccessionedSequence", "renderableClass" : "Protein", "position" : { "x" : 298, "y" : 658 }, "minX" : 262, "maxX" : 530, "minY" : 456, "maxY" : 917, "prop" : { "x" : 262, "y" : 646, "width" : 72, "height" : 25 }, "textPosition" : { "x" : 274, "y" : 648 }, "interactorsSummary" : { "type" : "TR", "shape" : { "c" : { "x" : 334, "y" : 646 }, "r" : 6, "type" : "CIRCLE", "empty" : true, "centre" : { "x" : 334, "y" : 646 } } }, "connectors" : [ { "edgeId" : 5089, "type" : "INPUT", "segments" : [ { "from" : { "x" : 312, "y" : 643 }, "to" : { "x" : 435, "y" : 542 } }, { "from" : { "x" : 435, "y" : 542 }, "to" : { "x" : 530, "y" : 544 } } ], "stoichiometry" : { "value" : 1 } }, { "edgeId" : 5092, "type" : "INPUT", "segments" : [ { "from" : { "x" : 337, "y" : 651 }, "to" : { "x" : 508, "y" : 619 } } ], "stoichiometry" : { "value" : 1 } }, { "edgeId" : 5095, "type" : "INPUT", "segments" : [ { "from" : { "x" : 299, "y" : 674 }, "to" : { "x" : 338, "y" : 911 } }, { "from" : { "x" : 338, "y" : 911 }, "to" : { "x" : 440, "y" : 917 } } ], "stoichiometry" : { "value" : 1 } }, { "edgeId" : 5084, "type" : "INPUT", "segments" : [ { "from" : { "x" : 304, "y" : 643 }, "to" : { "x" : 408, "y" : 456 } }, { "from" : { "x" : 408, "y" : 456 }, "to" : { "x" : 500, "y" : 457 } } ], "stoichiometry" : { "value" : 1 } } ] }, { "id" : 5086, "reactomeId" : 10836085, "displayName" : "TDG:AP-dsDNA", "schemaClass" : "Complex", "renderableClass" : "Complex", "position" : { "x" : 481, "y" : 425 }, "minX" : 427, "maxX" : 542, "minY" : 406, "maxY" : 457, "prop" : { "x" : 427, "y" : 412, "width" : 109, "height" : 26 }, "textPosition" : { "x" : 432, "y" : 417 }, "bgColor" : { "r" : 204, "g" : 255, "b" : 255 }, "interactorsSummary" : { "type" : "TR", "shape" : { "c" : { "x" : 536, "y" : 412 }, "r" : 6, "type" : "CIRCLE", "empty" : true, "centre" : { "x" : 536, "y" : 412 } } }, "connectors" : [ { "edgeId" : 5084, "type" : "INPUT", "segments" : [ { "from" : { "x" : 488, "y" : 441 }, "to" : { "x" : 500, "y" : 457 } } ], "stoichiometry" : { "value" : 1 } } ] }, { "id" : 5087, "reactomeId" : 10836258, "displayName" : "APEX1:AP-dsDNA", "schemaClass" : "Complex", "renderableClass" : "Complex", "position" : { "x" : 880, "y" : 593 }, "minX" : 598, "maxX" : 995, "minY" : 456, "maxY" : 926, "prop" : { "x" : 820, "y" : 581, "width" : 121, "height" : 24 }, "textPosition" : { "x" : 824, "y" : 584 }, "bgColor" : { "r" : 204, "g" : 255, "b" : 255 }, "interactorsSummary" : { "type" : "TR", "shape" : { "c" : { "x" : 941, "y" : 581 }, "r" : 6, "type" : "CIRCLE", "empty" : true, "centre" : { "x" : 941, "y" : 581 } } }, "connectors" : [ { "edgeId" : 5089, "type" : "OUTPUT", "segments" : [ { "from" : { "x" : 842, "y" : 578 }, "to" : { "x" : 719, "y" : 541 } }, { "from" : { "x" : 719, "y" : 541 }, "to" : { "x" : 627, "y" : 544 } } ], "stoichiometry" : { "value" : 1 }, "endShape" : { "a" : { "x" : 834, "y" : 580 }, "b" : { "x" : 842, "y" : 578 }, "c" : { "x" : 837, "y" : 572 }, "type" : "ARROW", "centre" : { "x" : 837, "y" : 572 } } }, { "edgeId" : 5092, "type" : "OUTPUT", "segments" : [ { "from" : { "x" : 817, "y" : 601 }, "to" : { "x" : 662, "y" : 624 } } ], "stoichiometry" : { "value" : 1 }, "endShape" : { "a" : { "x" : 811, "y" : 606 }, "b" : { "x" : 817, "y" : 601 }, "c" : { "x" : 810, "y" : 598 }, "type" : "ARROW", "centre" : { "x" : 810, "y" : 598 } } }, { "edgeId" : 5095, "type" : "OUTPUT", "segments" : [ { "from" : { "x" : 877, "y" : 608 }, "to" : { "x" : 806, "y" : 926 } }, { "from" : { "x" : 806, "y" : 926 }, "to" : { "x" : 663, "y" : 926 } } ], "stoichiometry" : { "value" : 1 }, "endShape" : { "a" : { "x" : 879, "y" : 616 }, "b" : { "x" : 877, "y" : 608 }, "c" : { "x" : 872, "y" : 614 }, "type" : "ARROW", "centre" : { "x" : 872, "y" : 614 } } }, { "edgeId" : 5098, "type" : "INPUT", "segments" : [ ], "stoichiometry" : { "value" : 1 } }, { "edgeId" : 5098, "type" : "CATALYST", "segments" : [ { "from" : { "x" : 908, "y" : 578 }, "to" : { "x" : 967, "y" : 556 } }, { "from" : { "x" : 967, "y" : 556 }, "to" : { "x" : 988, "y" : 579 } } ], "stoichiometry" : { "value" : 1 }, "endShape" : { "c" : { "x" : 991, "y" : 582 }, "r" : 4, "type" : "CIRCLE", "empty" : true, "centre" : { "x" : 991, "y" : 582 } } }, { "edgeId" : 5084, "type" : "OUTPUT", "segments" : [ { "from" : { "x" : 866, "y" : 578 }, "to" : { "x" : 722, "y" : 457 } }, { "from" : { "x" : 722, "y" : 457 }, "to" : { "x" : 598, "y" : 456 } } ], "stoichiometry" : { "value" : 1 }, "endShape" : { "a" : { "x" : 858, "y" : 577 }, "b" : { "x" : 866, "y" : 578 }, "c" : { "x" : 863, "y" : 570 }, "type" : "ARROW", "centre" : { "x" : 863, "y" : 570 } } } ] } ], "edges" : [ { "id" : 5089, "reactomeId" : 10836264, "displayName" : "Displacement of SMUG1 glycosylase by APEX1 at the AP site", "schemaClass" : "Reaction", "renderableClass" : "Reaction", "position" : { "x" : 583, "y" : 544 }, "minX" : 530, "maxX" : 627, "minY" : 538, "maxY" : 550, "reactionType" : "transition", "segments" : [ { "from" : { "x" : 530, "y" : 544 }, "to" : { "x" : 583, "y" : 544 } }, { "from" : { "x" : 583, "y" : 544 }, "to" : { "x" : 627, "y" : 544 } } ], "reactionShape" : { "a" : { "x" : 577, "y" : 538 }, "b" : { "x" : 589, "y" : 550 }, "type" : "BOX", "empty" : true, "centre" : { "x" : 583, "y" : 544 } }, "inputs" : [ { "id" : 5090, "points" : [ { "x" : 510, "y" : 514 } ] }, { "id" : 5085, "points" : [ { "x" : 312, "y" : 643 }, { "x" : 435, "y" : 542 } ] } ], "outputs" : [ { "id" : 5091, "points" : [ { "x" : 641, "y" : 521 } ] }, { "id" : 5087, "points" : [ { "x" : 842, "y" : 578 }, { "x" : 719, "y" : 541 } ] } ] }, { "id" : 5107, "reactomeId" : 10836298, "displayName" : "LIG1 binds APEX1 and PCNA at SSB", "schemaClass" : "Reaction", "renderableClass" : "Reaction", "position" : { "x" : 2461, "y" : 1183 }, "minX" : 2455, "maxX" : 2467, "minY" : 1177, "maxY" : 1212, "reactionType" : "binding", "segments" : [ { "from" : { "x" : 2460, "y" : 1183 }, "to" : { "x" : 2461, "y" : 1183 } }, { "from" : { "x" : 2461, "y" : 1183 }, "to" : { "x" : 2463, "y" : 1212 } } ], "endShape" : { "a" : { "x" : 2459, "y" : 1205 }, "b" : { "x" : 2463, "y" : 1212 }, "c" : { "x" : 2467, "y" : 1205 }, "type" : "ARROW", "centre" : { "x" : 2467, "y" : 1205 } }, "reactionShape" : { "c" : { "x" : 2461, "y" : 1183 }, "r" : 5, "type" : "CIRCLE", "centre" : { "x" : 2461, "y" : 1183 } }, "inputs" : [ { "id" : 5108, "points" : [ { "x" : 2459, "y" : 1147 } ] }, { "id" : 5109, "points" : [ { "x" : 2603, "y" : 1077 }, { "x" : 2517, "y" : 1181 } ] } ], "outputs" : [ { "id" : 5110 } ] }, { "id" : 5092, "reactomeId" : 10836266, "displayName" : "Displacement of NTHL1 glycosylase by APEX1 at the AP site", "schemaClass" : "Reaction", "renderableClass" : "Reaction", "position" : { "x" : 590, "y" : 625 }, "minX" : 508, "maxX" : 662, "minY" : 619, "maxY" : 631, "reactionType" : "transition", "segments" : [ { "from" : { "x" : 508, "y" : 619 }, "to" : { "x" : 590, "y" : 625 } }, { "from" : { "x" : 590, "y" : 625 }, "to" : { "x" : 662, "y" : 624 } } ], "reactionShape" : { "a" : { "x" : 584, "y" : 619 }, "b" : { "x" : 596, "y" : 631 }, "type" : "BOX", "empty" : true, "centre" : { "x" : 590, "y" : 625 } }, "inputs" : [ { "id" : 5093, "points" : [ { "x" : 496, "y" : 594 } ] }, { "id" : 5085, "points" : [ { "x" : 337, "y" : 651 } ] } ], "outputs" : [ { "id" : 5087, "points" : [ { "x" : 817, "y" : 601 } ] }, { "id" : 5094, "points" : [ { "x" : 674, "y" : 589 } ] } ] }, { "id" : 5095, "reactomeId" : 10836268, "displayName" : "Displacement of OGG1 glycosylase by APEX1 at the AP site", "schemaClass" : "Reaction", "renderableClass" : "Reaction", "position" : { "x" : 569, "y" : 920 }, "minX" : 440, "maxX" : 663, "minY" : 914, "maxY" : 926, "reactionType" : "transition", "segments" : [ { "from" : { "x" : 440, "y" : 917 }, "to" : { "x" : 569, "y" : 920 } }, { "from" : { "x" : 569, "y" : 920 }, "to" : { "x" : 663, "y" : 926 } } ], "reactionShape" : { "a" : { "x" : 563, "y" : 914 }, "b" : { "x" : 575, "y" : 926 }, "type" : "BOX", "empty" : true, "centre" : { "x" : 569, "y" : 920 } }, "inputs" : [ { "id" : 5096, "points" : [ { "x" : 428, "y" : 939 } ] }, { "id" : 5085, "points" : [ { "x" : 299, "y" : 674 }, { "x" : 338, "y" : 911 } ] } ], "outputs" : [ { "id" : 5087, "points" : [ { "x" : 877, "y" : 608 }, { "x" : 806, "y" : 926 } ] }, { "id" : 5097, "points" : [ { "x" : 683, "y" : 950 } ] } ] }, { "id" : 5111, "reactomeId" : 10879946, "displayName" : "LIG1 bound to APEX1 and PCNA ligates SSB", "schemaClass" : "Reaction", "renderableClass" : "Reaction", "position" : { "x" : 2470, "y" : 1318 }, "minX" : 2464, "maxX" : 2476, "minY" : 1274, "maxY" : 1351, "reactionType" : "transition", "segments" : [ { "from" : { "x" : 2466, "y" : 1274 }, "to" : { "x" : 2470, "y" : 1318 } }, { "from" : { "x" : 2470, "y" : 1318 }, "to" : { "x" : 2472, "y" : 1351 } } ], "endShape" : { "a" : { "x" : 2468, "y" : 1344 }, "b" : { "x" : 2472, "y" : 1351 }, "c" : { "x" : 2476, "y" : 1344 }, "type" : "ARROW", "centre" : { "x" : 2476, "y" : 1344 } }, "reactionShape" : { "a" : { "x" : 2464, "y" : 1312 }, "b" : { "x" : 2476, "y" : 1324 }, "type" : "BOX", "empty" : true, "centre" : { "x" : 2470, "y" : 1318 } }, "inputs" : [ { "id" : 5110 } ], "outputs" : [ { "id" : 5112 } ], "catalysts" : [ { "id" : 5110, "points" : [ { "x" : 2436, "y" : 1274 }, { "x" : 2413, "y" : 1294 } ] } ] }, { "id" : 5098, "reactomeId" : 10836275, "displayName" : "APEX1 mediates endonucleolytic cleavage at the 5' side of the AP site", "schemaClass" : "Reaction", "renderableClass" : "Reaction", "position" : { "x" : 999, "y" : 591 }, "minX" : 944, "maxX" : 1025, "minY" : 585, "maxY" : 597, "reactionType" : "transition", "segments" : [ { "from" : { "x" : 944, "y" : 591 }, "to" : { "x" : 999, "y" : 591 } }, { "from" : { "x" : 999, "y" : 591 }, "to" : { "x" : 1025, "y" : 591 } } ], "endShape" : { "a" : { "x" : 1018, "y" : 595 }, "b" : { "x" : 1025, "y" : 591 }, "c" : { "x" : 1018, "y" : 587 }, "type" : "ARROW", "centre" : { "x" : 1018, "y" : 587 } }, "reactionShape" : { "a" : { "x" : 993, "y" : 585 }, "b" : { "x" : 1005, "y" : 597 }, "type" : "BOX", "empty" : true, "centre" : { "x" : 999, "y" : 591 } }, "inputs" : [ { "id" : 5087 } ], "outputs" : [ { "id" : 5099 } ], "catalysts" : [ { "id" : 5087, "points" : [ { "x" : 908, "y" : 578 }, { "x" : 967, "y" : 556 } ] } ] }, { "id" : 5084, "reactomeId" : 10836260, "displayName" : "Displacement of TDG glycosylase by APEX1 at the AP site", "schemaClass" : "Reaction", "renderableClass" : "Reaction", "position" : { "x" : 567, "y" : 456 }, "minX" : 500, "maxX" : 598, "minY" : 450, "maxY" : 462, "reactionType" : "transition", "segments" : [ { "from" : { "x" : 500, "y" : 457 }, "to" : { "x" : 567, "y" : 456 } }, { "from" : { "x" : 567, "y" : 456 }, "to" : { "x" : 598, "y" : 456 } } ], "reactionShape" : { "a" : { "x" : 561, "y" : 450 }, "b" : { "x" : 573, "y" : 462 }, "type" : "BOX", "empty" : true, "centre" : { "x" : 567, "y" : 456 } }, "inputs" : [ { "id" : 5085, "points" : [ { "x" : 304, "y" : 643 }, { "x" : 408, "y" : 456 } ] }, { "id" : 5086, "points" : [ { "x" : 488, "y" : 441 } ] } ], "outputs" : [ { "id" : 5087, "points" : [ { "x" : 866, "y" : 578 }, { "x" : 722, "y" : 457 } ] }, { "id" : 5088, "points" : [ { "x" : 609, "y" : 440 } ] } ] }, { "id" : 5100, "reactomeId" : 10879917, "displayName" : "Oxidative damage to the AP site", "schemaClass" : "BlackBoxEvent", "renderableClass" : "Reaction", "position" : { "x" : 1133, "y" : 643 }, "minX" : 1127, "maxX" : 1139, "minY" : 609, "maxY" : 681, "reactionType" : "omitted", "segments" : [ { "from" : { "x" : 1133, "y" : 609 }, "to" : { "x" : 1133, "y" : 643 } }, { "from" : { "x" : 1133, "y" : 643 }, "to" : { "x" : 1135, "y" : 681 } } ], "endShape" : { "a" : { "x" : 1131, "y" : 674 }, "b" : { "x" : 1135, "y" : 681 }, "c" : { "x" : 1139, "y" : 674 }, "type" : "ARROW", "centre" : { "x" : 1139, "y" : 674 } }, "reactionShape" : { "a" : { "x" : 1127, "y" : 637 }, "b" : { "x" : 1139, "y" : 649 }, "s" : "\\\\", "type" : "BOX", "empty" : true, "centre" : { "x" : 1133, "y" : 643 } }, "inputs" : [ { "id" : 5099 } ], "outputs" : [ { "id" : 5101 } ] }, { "id" : 5102, "reactomeId" : 10836290, "displayName" : "POLD,POLE-mediated DNA strand displacement synthesis", "schemaClass" : "Reaction", "renderableClass" : "Reaction", "position" : { "x" : 1833, "y" : 1107 }, "minX" : 1779, "maxX" : 1870, "minY" : 1101, "maxY" : 1113, "reactionType" : "transition", "segments" : [ { "from" : { "x" : 1779, "y" : 1110 }, "to" : { "x" : 1833, "y" : 1107 } }, { "from" : { "x" : 1833, "y" : 1107 }, "to" : { "x" : 1870, "y" : 1106 } } ], "reactionShape" : { "a" : { "x" : 1827, "y" : 1101 }, "b" : { "x" : 1839, "y" : 1113 }, "type" : "BOX", "empty" : true, "centre" : { "x" : 1833, "y" : 1107 } }, "inputs" : [ { "id" : 5103, "points" : [ { "x" : 1720, "y" : 1111 } ] }, { "id" : 5104, "points" : [ { "x" : 1825, "y" : 1013 } ], "stoichiometry" : 10 } ], "outputs" : [ { "id" : 5105, "points" : [ { "x" : 1919, "y" : 1104 } ] }, { "id" : 5106, "points" : [ { "x" : 1915, "y" : 1012 } ], "stoichiometry" : 10 } ], "catalysts" : [ { "id" : 5103, "points" : [ { "x" : 1720, "y" : 1134 }, { "x" : 1763, "y" : 1147 } ] } ] } ], "compartments" : [ { "id" : 5139, "reactomeId" : 5460, "displayName" : "mitochondrial matrix", "schemaClass" : "Compartment", "renderableClass" : "Compartment", "position" : { "x" : 505, "y" : 120 }, "minX" : 349, "maxX" : 661, "minY" : 27, "maxY" : 214, "prop" : { "x" : 349, "y" : 27, "width" : 312, "height" : 187 }, "textPosition" : { "x" : 483, "y" : 48 }, "insets" : { "x" : 359, "y" : 37, "width" : 292, "height" : 167 }, "bgColor" : { "r" : 250, "g" : 240, "b" : 240 } }, { "id" : 5140, "reactomeId" : 70101, "displayName" : "cytosol", "schemaClass" : "Compartment", "renderableClass" : "Compartment", "position" : { "x" : 1436, "y" : 795 }, "minX" : 0, "maxX" : 2872, "minY" : 0, "maxY" : 1590, "prop" : { "x" : 0, "y" : 0, "width" : 2872, "height" : 1590 }, "textPosition" : { "x" : 124, "y" : 44 }, "insets" : { "x" : 10, "y" : 10, "width" : 2852, "height" : 1570 }, "bgColor" : { "r" : 250, "g" : 240, "b" : 240 }, "componentIds" : [ 5113, 5139 ] }, { "id" : 5113, "reactomeId" : 7660, "displayName" : "nucleoplasm", "schemaClass" : "Compartment", "renderableClass" : "Compartment", "position" : { "x" : 1434, "y" : 908 }, "minX" : 46, "maxX" : 2823, "minY" : 277, "maxY" : 1540, "prop" : { "x" : 46, "y" : 277, "width" : 2777, "height" : 1263 }, "textPosition" : { "x" : 111, "y" : 301 }, "insets" : { "x" : 56, "y" : 287, "width" : 2757, "height" : 1243 }, "bgColor" : { "r" : 250, "g" : 240, "b" : 240 }, "componentIds" : [ 5097, 5088, 5086, 5091, 5094, 5093, 5087, 5085, 5089, 5092, 5095, 5098, 5099, 5116, 5084, 5090, 5096, 5141, 5100, 5101, 5104, 5106, 5109, 5103, 5102, 5105, 5108, 5107, 5110, 5112, 5111 ] } ], "notes" : [ ], "links" : [ { "id" : 5141, "renderableClass" : "Interaction", "position" : { "x" : 244, "y" : 659 }, "minX" : 229, "maxX" : 259, "minY" : 653, "maxY" : 665, "interactionType" : "Activate", "segments" : [ { "from" : { "x" : 229, "y" : 660 }, "to" : { "x" : 259, "y" : 659 } } ], "endShape" : { "a" : { "x" : 252, "y" : 663 }, "b" : { "x" : 259, "y" : 659 }, "c" : { "x" : 252, "y" : 655 }, "type" : "ARROW", "empty" : true, "centre" : { "x" : 252, "y" : 655 } }, "reactionShape" : { "a" : { "x" : 238, "y" : 653 }, "b" : { "x" : 250, "y" : 665 }, "type" : "BOX", "empty" : true, "centre" : { "x" : 244, "y" : 659 } }, "inputs" : [ { "id" : 5116 } ], "outputs" : [ { "id" : 5085 } ] } ], "shadows" : [ { "id" : 5142, "reactomeId" : 10910988, "displayName" : "Displacement of DNA glycosylase by APEX1", "schemaClass" : "Pathway", "renderableClass" : "Shadow", "position" : { "x" : 601, "y" : 693 }, "minX" : 252, "maxX" : 951, "minY" : 402, "maxY" : 984, "prop" : { "x" : 252, "y" : 402, "width" : 699, "height" : 582 }, "points" : [ { "x" : 252, "y" : 402 }, { "x" : 951, "y" : 402 }, { "x" : 951, "y" : 984 }, { "x" : 252, "y" : 984 } ], "colour" : "#4684ee" }, { "id" : 5143, "reactomeId" : 10910994, "displayName" : "Resolution of AP sites via the multiple-nucleotide patch replacement pathway", "schemaClass" : "Pathway", "renderableClass" : "Shadow", "position" : { "x" : 1832, "y" : 986 }, "minX" : 1018, "maxX" : 2646, "minY" : 572, "maxY" : 1401, "prop" : { "x" : 1018, "y" : 572, "width" : 1628, "height" : 829 }, "points" : [ { "x" : 1018, "y" : 572 }, { "x" : 2646, "y" : 572 }, { "x" : 2646, "y" : 1401 }, { "x" : 1018, "y" : 1401 } ], "colour" : "#dc3912" } ], "minX" : 0, "maxX" : 2872, "minY" : 0, "maxY" : 1590, "disease" : false }