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PDBsum entry 3jap
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Top Page protein dna_rna ligands metals Protein-protein interface(s) pores links
Pore analysis for: 3jap calculated with MOLE 2.0 PDB id
3jap
Pores calculated on whole structure Pores calculated excluding ligands
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31 pores, coloured by radius 30 pores, coloured by radius 30 pores, coloured as in
list below
Pores are connected internal spaces going through the structure. Only pores longer than 25 Å are shown.
Pores
Free R
Length
HPathy
HPhob
Polar
Rel Mut
Residue..type
Ligands
Radius
1 3.51 4.90 93.7 -2.10 -0.31 29.1 77 11 10 7 5 6 2 0  U 1059 2 U 1060 2
2 1.65 1.69 110.6 -1.51 -0.62 17.9 83 9 5 4 3 2 1 0  A 1165 2 G 1166 2 U 1167 2 U 1361 2 A 1467 2 C
1468 2 A 1473 2 C 1474 2 A 1524 2 C 1525 2 U 1526
2 C 1527 2 C 1528 2 G 1529 2 U 1530 2 A 1571 2 G
1572 2 C 1587 2 MG 1869 2
3 2.29 2.29 132.5 -1.36 -0.53 16.1 81 11 1 5 4 3 0 0  C 32 1 G 1149 2 A 1151 2 G 1152 2 C 1161 2 G 1163
2 G 1164 2 A 1165 2 A 1571 2 G 1572 2 A 1575 2 U
1576 2 C 1617 2 C 1618 2 U 1796 2 U 1797 2 A 1798
2 A 3 3 U 4 3 C 5 3 U 6 3 U 8 3 C 9 3 U 10 3 C 11
3 U 12 3
4 2.29 2.33 132.3 -1.23 -0.54 14.9 83 10 3 4 6 2 1 0  C 32 1 U 33 1 C 34 1 A 35 1 A 11 2 G 551 2 A 555
2 U 557 2 C 574 2 U 580 2 A 1146 2 C 1147 2 G
1148 2 C 1161 2 G 1163 2 G 1164 2 A 1165 2 U 1282
2 C 1424 2 A 1425 2 A 1571 2 G 1572 2 A 1575 2 U
1576 2 C 1618 2 U 1619 2 G 1620 2 C 1621 2 C 1632
2 A 1633 2 C 1634 2 C 1635 2 MG 1803 2 C 11 3 U
12 3
5 2.32 2.33 137.4 -1.17 -0.53 15.2 84 10 2 1 5 2 0 0  C 32 1 G 1149 2 A 1151 2 G 1152 2 C 1161 2 G 1163
2 G 1164 2 A 1165 2 A 1571 2 G 1572 2 A 1575 2 U
1576 2 C 1617 2 C 1618 2 U 1796 2 U 1797 2 A 1798
2 A 3 3 U 4 3 C 5 3 U 6 3 U 8 3 C 9 3 U 10 3 C 11
3 U 12 3
6 1.33 1.57 167.4 -1.07 -0.31 14.1 85 13 6 12 11 5 3 0  U 1053 2 U 1054 2 U 1059 2 U 1060 2
7 2.36 2.36 175.0 -0.98 -0.57 12.4 85 11 3 5 7 1 2 0  U 8 2 U 9 2 G 10 2 A 11 2 G 551 2 A 555 2 U 557 2
G 573 2 C 574 2 U 580 2 G 1040 2 G 1041 2 A 1042
2 C 1077 2 U 1078 2 U 1079 2 A 1138 2 G 1139 2 G
1140 2 A 1141 2 A 1142 2 U 1143 2 U 1144 2 G 1294
2 A 1295 2 U 1301 2 A 1320 2 U 1625 2 U 1626 2 G
1627 2 U 1628 2 A 1629 2 C 1630 2 A 1631 2 C 1632
2 C 1638 2 A 1798 2 MG 1803 2 MG 1810 2 MG 1851 2
A 3 3
8 1.26 1.28 198.8 -0.96 -0.47 12.7 85 15 6 9 16 1 5 0  G 1349 2 G 1350 2 U 1351 2 U 1352 2 U 1362 2 G
1363 2 C 1364 2 C 1365 2 G 1366 2 G 1367 2 C 1479
2 G 1519 2
9 1.27 1.81 206.8 0.09 -0.04 11.4 80 11 2 3 23 4 1 0  G 551 2 A 555 2 U 557 2 C 574 2 G 575 2 G 576 2 U
577 2 A 578 2 U 580 2 C 1247 2 U 1248 2 U 1249 2
U 1250 2 C 1251 2 U 1252 2 G 1260 2 G 1270 2 U
1271 2 G 1272 2 C 1273 2 A 1274 2 A 1425 2 C 1439
2 U 1440 2 U 1441 2 G 1443 2 MG 1803 2
10 1.99 1.99 208.8 -0.90 -0.57 13.3 82 11 6 4 5 1 0 0  G 9 1 A 21 1 C 23 1 G 24 1 C 25 1 G 26 1 C 27 1 A
28 1 G 29 1 G 30 1 U 36 1 A 37 1 A 38 1 C 40 1 C
41 1 U 42 1 G 43 1 A 46 2 A 409 2 C 410 2 G 1570
2 A 1571 2 U 1645 2 A 1646 2 G 1647 2 U 1648 2 A
1649 2 A 1657 2 A 1658 2 U 1659 2 G 1660 2 U 1732
2 U 1733 2 G 1734 2 G 1735 2 U 1740 2 U 1741 2 A
1742 2 G 1743 2
11 1.87 3.03 212.9 -0.80 -0.43 15.1 81 11 7 5 7 2 0 1  G 9 1 A 21 1 C 23 1 G 24 1 C 25 1 G 26 1 C 27 1 A
28 1 G 29 1 G 30 1 U 36 1 A 37 1 A 38 1 C 40 1 C
41 1 U 42 1 G 43 1 A 46 2 C 432 2 G 1570 2 A 1571
2 U 1645 2 A 1646 2 G 1647 2 U 1648 2 A 1649 2 A
1658 2 U 1741 2 A 1742 2 G 1743 2
12 1.20 1.37 230.7 -0.56 -0.35 11.7 82 12 7 6 22 2 1 0  A 1 1 G 2 1 C 3 1 G 4 1 C 5 1 C 6 1 G 9 1 G 15 1
U 16 1 G 18 1 A 21 1 G 22 1 C 23 1 G 24 1 G 43 1
C 61 1 C 62 1 G 63 1 A 64 1 G 65 1 C 66 1 G 1570
2 A 1571 2
13 1.24 2.11 230.5 -0.40 -0.31 11.5 77 15 2 5 20 3 1 0  G 9 1 A 21 1 C 23 1 G 24 1 C 25 1 G 26 1 C 27 1 A
28 1 G 29 1 G 30 1 U 36 1 A 37 1 A 38 1 C 40 1 C
41 1 U 42 1 G 43 1 G 1178 2 C 1179 2 U 1180 2 U
1181 2 A 1182 2 A 1183 2 A 1210 2 G 1211 2 G 1212
2 U 1238 2 U 1239 2 U 1246 2 C 1247 2 U 1248 2 U
1249 2 U 1250 2 C 1251 2 U 1252 2 G 1570 2 A 1571
2
14 1.23 1.56 243.9 -1.19 -0.46 14.2 86 18 4 14 11 4 2 0  G 1152 2 G 1153 2 G 1154 2 U 1309 2 U 1390 2 G
1392 2 G 1393 2 U 1394 2 C 1402 2 G 1403 2 A 1404
2 U 1405 2 G 1406 2 G 1614 2 C 1616 2 U 1796 2 U
1797 2 A 1798 2 A 3 3 U 4 3 C 5 3 U 6 3 U 8 3
15 1.22 1.22 244.0 -0.60 -0.37 13.7 85 17 5 4 14 2 0 0  A 1 1 G 2 1 C 3 1 G 4 1 C 5 1 C 6 1 G 15 1 U 16 1
G 18 1 G 22 1 C 23 1 G 24 1 C 32 1 A 39 1 C 61 1
C 62 1 G 63 1 A 64 1 G 65 1 C 66 1 U 998 2 C 999
2 A 1000 2 G 1149 2 A 1151 2 G 1152 2 C 1617 2 C
1618 2 U 1796 2 U 1797 2 A 1798 2 A 3 3 U 4 3 C 5
3 U 6 3 U 8 3 C 9 3 U 10 3 C 11 3 U 12 3
16 1.23 1.57 254.8 -1.01 -0.51 12.1 88 15 5 11 12 3 2 0  C 32 1 G 1149 2 A 1151 2 G 1152 2 G 1153 2 G 1154
2 C 1161 2 G 1163 2 G 1164 2 A 1165 2 U 1309 2 U
1390 2 G 1392 2 G 1393 2 U 1394 2 C 1402 2 G 1403
2 A 1404 2 U 1405 2 G 1406 2 A 1571 2 G 1572 2 A
1575 2 U 1576 2 G 1614 2 C 1616 2 C 1617 2 C 1618
2 C 9 3 U 10 3 C 11 3 U 12 3
17 1.99 1.99 250.9 -1.23 -0.73 11.4 86 9 3 8 2 1 0 0  C 313 2 A 314 2 A 315 2 C 316 2 U 317 2 U 318 2 C
320 2 U 872 2 C 873 2 G 876 2 G 877 2 G 878 2 C
879 2 A 880 2 U 881 2 C 926 2 C 942 2 A 943 2 U
944 2 U 946 2 G 947 2 C 948 2 A 950 2 A 951 2 A
972 2 A 973 2 C 974 2 G 975 2 A 976 2 A 977 2 U
1016 2 A 1019 2 C 1020 2 C 1021 2 A 1022 2 U 1056
2 U 1057 2 U 1062 2 G 1063 2 U 1119 2 C 1120 2 G
1121 2 A 1657 2 A 1658 2 U 1659 2 G 1660 2 G 1661
2 C 1662 2 U 1663 2 U 1664 2 A 1728 2 A 1729 2 A
1730 2 C 1731 2 U 1732 2 U 1733 2 G 1734 2 G 1735
2 U 1736 2 C 1737 2 A 1798 2 A 3 3 UNK 118 p UNK
122 p UNK 125 p UNK 141 p UNK 145 p UNK 150 p UNK
153 p UNK 157 p
18 1.91 2.20 261.7 -1.11 -0.68 11.9 84 10 5 9 4 1 0 1  A 46 2 U 101 2 U 102 2 C 313 2 A 314 2 A 315 2 C
316 2 U 317 2 G 354 2 G 355 2 G 356 2 U 357 2 C
432 2 U 872 2 C 873 2 G 876 2 G 877 2 G 878 2 C
879 2 A 880 2 U 881 2 C 926 2 C 942 2 A 943 2 U
944 2 U 946 2 G 947 2 C 948 2 A 950 2 A 951 2 A
972 2 A 973 2 C 974 2 G 975 2 A 976 2 A 977 2 U
1016 2 A 1019 2 C 1020 2 C 1021 2 A 1022 2 U 1056
2 U 1057 2 U 1062 2 G 1063 2 U 1119 2 C 1120 2 G
1121 2 A 1658 2 U 1659 2 G 1660 2 G 1661 2 C 1662
2 U 1736 2 C 1737 2 U 1739 2 U 1740 2 A 1798 2 A
3 3 UNK 118 p UNK 122 p UNK 125 p UNK 145 p UNK
150 p UNK 153 p UNK 157 p
19 1.29 1.52 282.6 -1.10 -0.50 13.4 86 21 6 14 13 4 3 0  G 551 2 A 555 2 U 557 2 U 580 2 C 1155 2 A 1156 2
C 1157 2 G 1276 2 C 1278 2 C 1279 2 G 1280 2 U
1281 2 U 1284 2 U 1285 2 U 1309 2 U 1310 2 A 1311
2 U 1390 2 G 1392 2 G 1393 2 U 1394 2 C 1402 2 G
1403 2 A 1404 2 U 1405 2 G 1406 2 U 1411 2 U 1412
2 A 1415 2 G 1416 2 G 1417 2 A 1419 2 A 1420 2 A
1423 2 C 1424 2 C 1613 2 G 1614 2 U 1615 2 MG
1803 2
20 1.28 1.28 313.7 -1.01 -0.46 16.3 85 17 11 9 19 2 1 0  A 1 1 G 2 1 C 3 1 C 11 1 G 12 1 G 26 1 C 27 1 A
28 1 A 44 1 U 45 1 G 46 1 C 69 1 G 70 1 C 71 1 U
72 1 A 73 1 C 74 1 C 75 1 A 76 1 U 1361 2 C 1459
2 G 1460 2 G 1529 2 U 1530 2 C 1531 2 G 1532 2 U
1533 2 G 1534 2 C 1535 2 U 1536 2 C 1566 2 A 1567
2 A 1568 2
21 1.45 1.45 315.6 -1.20 -0.49 18.3 83 20 13 10 12 2 1 1  G 26 1 C 27 1 A 28 1 A 44 1 U 45 1 G 46 1 A 46 2
C 432 2 U 1361 2 C 1459 2 G 1460 2 G 1529 2 U
1530 2 C 1531 2 G 1532 2 U 1533 2 G 1534 2 C 1535
2 U 1536 2 C 1566 2 A 1567 2 A 1568 2 U 1645 2 A
1646 2 G 1647 2 U 1648 2 A 1649 2 A 1658 2 U 1741
2 A 1742 2 G 1743 2
22 2.15 2.15 313.3 -0.82 -0.58 10.0 86 16 1 6 8 2 0 0  G 9 1 A 21 1 C 23 1 G 24 1 C 25 1 G 26 1 A 39 1 C
40 1 C 41 1 U 42 1 G 43 1 U 193 2 U 215 2 A 216 2
U 222 2 C 223 2 A 225 2 U 226 2 G 234 2 C 236 2 A
315 2 U 348 2 U 349 2 U 628 2 A 629 2 G 630 2 G
739 2 A 740 2 U 742 2 U 807 2 G 808 2 A 810 2 A
828 2 U 829 2 U 831 2 U 832 2 G 833 2 U 834 2 U
835 2 G 836 2 G 837 2 U 838 2 U 839 2 G 844 2 G
845 2 A 846 2 C 847 2 A 970 2 G 971 2 U 980 2 U
981 2 A 992 2 G 993 2 A 994 2 U 995 2 G 996 2 C
999 2 G 1001 2 A 1002 2 U 1003 2 U 1119 2 C 1120
2 G 1121 2 C 1122 2 A 1123 2 G 1570 2 A 1571 2 G
1775 2 G 1776 2 U 1777 2 UNK 121 p UNK 125 p UNK
145 p UNK 148 p UNK 150 p UNK 152 p UNK 153 p UNK
155 p UNK 156 p
23 2.33 2.37 327.4 -0.84 -0.57 10.4 85 17 1 5 9 3 0 0  G 9 1 A 21 1 C 23 1 G 24 1 C 25 1 G 26 1 A 39 1 C
40 1 C 41 1 U 42 1 G 43 1 A 180 2 A 181 2 U 202 2
U 204 2 A 205 2 U 206 2 U 207 2 U 208 2 U 210 2 U
211 2 A 212 2 G 213 2 A 214 2 U 215 2 A 216 2 U
248 2 C 249 2 A 250 2 A 253 2 U 254 2 A 315 2 U
348 2 U 349 2 U 628 2 A 629 2 G 630 2 G 739 2 A
740 2 U 742 2 U 807 2 G 808 2 A 810 2 G 844 2 G
845 2 A 846 2 C 847 2 A 970 2 G 971 2 U 980 2 U
981 2 A 992 2 G 993 2 A 994 2 U 995 2 G 996 2 C
999 2 G 1001 2 A 1002 2 U 1003 2 U 1119 2 C 1120
2 G 1121 2 C 1122 2 A 1123 2 G 1570 2 A 1571 2 G
1775 2 G 1776 2 U 1777 2 MG 1858 2 UNK 121 p UNK
125 p UNK 145 p UNK 148 p UNK 150 p UNK 152 p UNK
153 p UNK 155 p UNK 156 p
24 1.34 2.72 321.7 -0.50 -0.26 14.1 78 18 8 7 25 5 1 1  A 46 2 C 432 2 G 1178 2 C 1179 2 U 1180 2 U 1181
2 A 1182 2 A 1183 2 A 1210 2 G 1211 2 G 1212 2 U
1238 2 U 1239 2 U 1246 2 C 1247 2 U 1248 2 U 1249
2 U 1250 2 C 1251 2 U 1252 2 U 1645 2 A 1646 2 G
1647 2 U 1648 2 A 1649 2 A 1658 2 U 1741 2 A 1742
2 G 1743 2
25 1.34 1.62 358.0 -0.71 -0.30 14.1 80 21 7 9 29 4 2 0  A 1 1 G 2 1 C 3 1 C 69 1 G 70 1 C 71 1 U 72 1 A
73 1 C 74 1 C 75 1 A 76 1 U 1180 2 U 1181 2 A
1182 2 A 1183 2 A 1210 2 G 1211 2 G 1212 2 A 1237
2 U 1238 2 U 1239 2 U 1246 2 C 1247 2 U 1248 2 U
1249 2 U 1250 2 C 1251 2 U 1252 2
26 1.36 2.30 357.0 -0.50 -0.39 10.5 78 16 2 7 23 5 2 0  A 618 2 A 1025 2 G 1040 2 G 1041 2 A 1042 2 C
1077 2 U 1078 2 U 1079 2 G 1109 2 G 1110 2 A 1138
2 G 1139 2 G 1140 2 A 1141 2 A 1142 2 U 1143 2 U
1144 2 G 1178 2 C 1179 2 U 1180 2 U 1181 2 A 1182
2 A 1183 2 A 1210 2 G 1211 2 G 1212 2 U 1238 2 U
1239 2 U 1246 2 C 1247 2 U 1248 2 U 1249 2 U 1250
2 C 1251 2 U 1252 2 G 1294 2 A 1295 2 U 1301 2 A
1320 2 U 1625 2 U 1626 2 G 1627 2 U 1628 2 A 1629
2 C 1638 2 C 1639 2 A 1751 2 A 1752 2 A 1753 2 A
1754 2 G 1755 2 U 1756 2 G 1790 2 G 1791 2 A 1798
2 MG 1825 2 G 15 3 C 16 3
27 1.45 1.44 368.1 -0.75 -0.51 9.9 85 16 6 12 13 4 3 1  A 46 2 U 310 2 A 311 2 U 312 2 C 313 2 A 358 2 C
432 2 A 618 2 A 619 2 A 620 2 A 1025 2 G 1106 2 G
1107 2 G 1110 2 G 1113 2 G 1129 2 A 1130 2 G 1140
2 A 1141 2 A 1142 2 U 1143 2 U 1144 2 G 1145 2 A
1146 2 C 1147 2 G 1148 2 G 1149 2 A 1150 2 A 1151
2 G 1152 2 G 1153 2 G 1154 2 U 1309 2 U 1390 2 G
1392 2 G 1393 2 U 1394 2 C 1402 2 G 1403 2 A 1404
2 U 1405 2 G 1406 2 G 1614 2 C 1616 2 C 1617 2 C
1621 2 C 1622 2 C 1623 2 U 1624 2 U 1625 2 U 1626
2 G 1627 2 U 1628 2 A 1629 2 C 1650 2 A 1658 2 U
1739 2 U 1740 2 U 1741 2 G 1790 2 G 1791 2 MG
1825 2 MG 1830 2
28 1.45 1.46 394.8 -0.74 -0.61 8.4 87 14 4 10 11 3 3 0  C 313 2 A 314 2 A 315 2 C 316 2 U 317 2 U 318 2 C
320 2 A 618 2 A 620 2 A 621 2 A 622 2 G 623 2 C
624 2 G 971 2 A 972 2 A 1022 2 U 1023 2 A 1024 2
A 1025 2 G 1113 2 U 1119 2 C 1120 2 C 1127 2 U
1128 2 G 1140 2 A 1141 2 A 1142 2 U 1143 2 U 1144
2 G 1145 2 A 1146 2 C 1147 2 G 1148 2 G 1149 2 A
1150 2 A 1151 2 G 1152 2 G 1153 2 G 1154 2 U 1309
2 U 1390 2 G 1392 2 G 1393 2 U 1394 2 C 1402 2 G
1403 2 A 1404 2 U 1405 2 G 1406 2 G 1614 2 C 1616
2 C 1617 2 C 1621 2 C 1622 2 C 1623 2 U 1624 2 U
1625 2 U 1626 2 G 1627 2 U 1628 2 A 1629 2 A 1657
2 A 1658 2 U 1659 2 G 1660 2 G 1661 2 C 1662 2 U
1663 2 U 1664 2 A 1728 2 A 1729 2 A 1730 2 C 1731
2 U 1732 2 U 1733 2 G 1734 2 G 1735 2 U 1736 2 C
1737 2 C 1770 2 C 1771 2 G 1772 2 G 1790 2 G 1791
2 MG 1805 2 MG 1825 2 UNK 141 p UNK 145 p UNK 150
p UNK 153 p UNK 156 p
29 1.29 1.54 450.0 -0.75 -0.55 9.3 87 21 4 12 16 5 3 0  A 180 2 A 181 2 U 202 2 U 204 2 A 205 2 U 206 2 U
207 2 U 208 2 U 210 2 U 211 2 A 212 2 G 213 2 A
214 2 U 215 2 A 216 2 U 248 2 C 249 2 A 250 2 A
253 2 U 254 2 A 315 2 U 348 2 U 349 2 A 618 2 A
620 2 A 621 2 A 622 2 G 623 2 C 624 2 U 628 2 A
629 2 G 630 2 G 739 2 A 740 2 U 742 2 U 807 2 G
808 2 A 810 2 G 844 2 G 845 2 A 846 2 C 847 2 A
970 2 G 971 2 A 972 2 A 1022 2 U 1023 2 A 1024 2
A 1025 2 G 1113 2 U 1119 2 C 1120 2 C 1127 2 U
1128 2 G 1140 2 A 1141 2 A 1142 2 U 1143 2 U 1144
2 G 1145 2 A 1146 2 C 1147 2 G 1148 2 G 1149 2 A
1150 2 A 1151 2 G 1152 2 G 1153 2 G 1154 2 U 1309
2 U 1390 2 G 1392 2 G 1393 2 U 1394 2 C 1402 2 G
1403 2 A 1404 2 U 1405 2 G 1406 2 G 1614 2 C 1616
2 C 1617 2 C 1621 2 C 1622 2 C 1623 2 U 1624 2 U
1625 2 U 1626 2 G 1627 2 U 1628 2 A 1629 2 C 1770
2 C 1771 2 G 1772 2 G 1790 2 G 1791 2 MG 1805 2
MG 1825 2 MG 1858 2 UNK 152 p UNK 155 p UNK 156 p
30 1.34 2.44 485.9 -0.64 -0.39 11.8 81 28 5 10 31 8 1 0  A 180 2 A 181 2 U 202 2 U 204 2 A 205 2 U 206 2 U
207 2 U 208 2 U 210 2 U 211 2 A 212 2 G 213 2 A
214 2 U 215 2 A 216 2 U 248 2 C 249 2 A 250 2 A
253 2 U 254 2 A 315 2 U 348 2 U 349 2 U 628 2 A
629 2 G 630 2 G 739 2 A 740 2 U 742 2 U 807 2 G
808 2 A 810 2 G 844 2 G 845 2 A 846 2 C 847 2 A
970 2 G 971 2 U 981 2 U 1119 2 C 1120 2 G 1121 2
C 1122 2 A 1123 2 G 1178 2 C 1179 2 U 1180 2 U
1181 2 A 1182 2 A 1183 2 A 1210 2 G 1211 2 G 1212
2 U 1238 2 U 1239 2 U 1246 2 C 1247 2 U 1248 2 U
1249 2 U 1250 2 C 1251 2 U 1252 2 G 1643 2 C 1644
2 G 1746 2 A 1747 2 G 1776 2 U 1777 2 MG 1858 2
UNK 121 p UNK 125 p UNK 145 p UNK 148 p UNK 150 p
UNK 152 p UNK 153 p UNK 155 p UNK 156 p

Residue-type_colouring
Positive Negative Neutral Aliphatic Aromatic Pro & Gly Cysteine
H,K,R D,E S,T,N,Q A,V,L,I,M F,Y,W P,G C

Acknowledgement
Pores were calculated by MOLE 2.0 program version 2.5.13.11.08 and visualized using Pymol 0.97rc.
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