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PDBsum entry 2gyb
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Top Page protein dna_rna Protein-protein interface(s) pores links
Pore analysis for: 2gyb calculated with MOLE 2.0 PDB id
2gyb
Pores calculated on whole structure Pores calculated excluding ligands
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30 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 3.47 3.47 61.7 -1.30 -0.78 12.1 75 3 2 2 0 0 1 0  A 994 A C 995 A A 996 A G 1002 A G 1003 A U 1007
A U 1008 A U 1017 A A 1019 A G 1020 A A 1021 A A
1022 A C 1038 A G 1039 A U 1040 A G 1041 A G 1047
A A 1204 A
2 1.99 2.16 64.8 -0.91 -0.59 12.0 87 5 0 0 2 0 0 0  C 1112 A C 1113 A C 1114 A U 1115 A U 1116 A A
1117 A U 1118 A C 1119 A C 1120 A U 1148 A A 1151
A A 1152 A G 1153 A G 1154 A A 1155 A G 1156 A A
1157 A C 1158 A G 1177 A G 1178 A A 1179 A
3 2.57 2.67 70.3 -1.81 -0.64 19.9 87 8 0 1 0 0 0 0  C 1096 A C 1097 A C 1098 A G 1099 A C 1100 A G
1104 A A 1105 A G 1106 A G 1108 A C 1109 A A 1110
A A 1111 A G 1156 A A 1157 A C 1158 A U 1159 A G
1160 A A 1171 A
4 1.19 1.19 72.6 -0.69 -0.72 6.5 73 2 1 0 0 1 0 0  A 949 A U 950 A U 952 A G 953 A G 954 A U 955 A U
956 A U 957 A A 958 A A 959 A U 960 A U 961 A C
962 A C 985 A U 986 A G 1222 A U 1224 A A 1225 A
C 1226 A C 1320 A U 1321 A
5 2.24 2.24 83.7 -0.77 -0.82 6.1 80 1 1 1 0 0 0 0  U 957 A A 958 A A 959 A C 962 A G 963 A U 982 A A
983 A C 984 A A 994 A C 995 A A 996 A G 1047 A G
1048 A U 1049 A G 1050 A C 1051 A A 1204 A U 1205
A C 1214 A G 1215 A A 1216 A G 22 U G 30 U A 31 U
G 42 U G 43 U A 44 U
6 3.62 3.62 87.1 -0.87 -0.66 7.6 75 3 1 0 0 1 1 0  G 947 A C 948 A U 956 A U 957 A G 1222 A U 1224 A
A 1225 A C 1226 A A 1227 A C 1228 A A 1229 A C
1320 A U 1321 A G 20 U A 21 U G 22 U G 43 V A 44
V G 45 V
7 2.83 2.92 90.9 -0.45 -0.10 8.6 78 5 1 3 5 4 1 0  A 996 A G 1047 A G 1058 A C 1112 A C 1113 A C
1114 A A 1152 A G 1153 A G 1154 A A 1155 A G 1156
A A 1157 A C 1158 A G 1160 A C 1203 A A 1204 A
8 2.77 2.88 101.3 -0.13 -0.20 10.4 78 6 3 2 8 2 2 1  G 1002 A G 1003 A U 1007 A U 1008 A U 1009 A U
1010 A A 1012 A G 1013 A G 1015 A A 1016 A U 1017
A G 1018 A A 1019 A G 1020 A A 1021 A A 1022 A G
1039 A U 1040 A G 1041 A G 1312 A U 1313 A C 1314
A U 1315 A G 1316 A C 1317 A A 1318 A
9 1.63 1.63 101.0 -0.76 -0.76 7.9 83 3 0 0 0 0 0 0  G 929 A C 930 A C 931 A C 932 A G 933 A A 1067 A
G 1088 A G 1089 A U 1090 A U 1091 A A 1092 A A
1093 A C 1109 A A 1110 A A 1111 A G 1156 A A 1157
A C 1158 A U 1159 A G 1160 A A 1171 A U 1173 A U
1183 A C 1378 A U 1380 A C 1533 A
10 2.24 4.81 101.2 -1.32 -0.27 22.0 86 8 5 6 10 0 1 0  G 1047 A A 1204 A U 1205 A
11 2.37 2.60 104.1 -0.65 -0.30 14.7 80 10 4 2 6 1 1 1  C 980 A U 981 A C 995 A A 996 A G 1047 A G 1048 A
U 1049 A A 1204 A U 1205 A G 1312 A U 1313 A C
1314 A U 1315 A G 1316 A C 1317 A A 1318 A A 1360
A
12 2.24 2.24 119.7 -0.72 -0.78 7.1 72 3 1 1 0 0 1 0  U 957 A A 958 A A 959 A C 962 A G 963 A U 982 A A
983 A C 984 A A 994 A C 995 A A 996 A G 1002 A G
1003 A U 1007 A U 1008 A U 1017 A A 1019 A G 1020
A A 1021 A A 1022 A C 1038 A G 1039 A U 1040 A G
1041 A G 1048 A U 1049 A G 1050 A C 1051 A C 1214
A G 1215 A A 1216 A G 22 U G 30 U A 31 U G 42 U G
43 U A 44 U
13 1.63 1.63 133.7 -0.78 -0.68 8.8 85 6 0 1 2 0 0 0  G 929 A C 930 A C 931 A C 932 A G 933 A G 1088 A
G 1089 A U 1090 A U 1091 A A 1092 A A 1111 A C
1112 A C 1114 A U 1115 A U 1116 A A 1117 A U 1118
A C 1119 A C 1120 A U 1148 A A 1151 A A 1152 A G
1153 A G 1154 A A 1155 A G 1156 A U 1173 A G 1177
A G 1178 A A 1179 A G 1182 A U 1183 A G 1184 A G
1185 A G 1186 A G 1187 A A 1377 A C 1378 A U 1380
A C 1533 A
14 1.98 1.98 140.0 -0.70 -0.77 6.6 81 3 1 0 0 0 2 0  G 953 A G 954 A U 956 A U 957 A G 966 A C 967 A A
968 A U 1062 A U 1065 A C 1066 A A 1110 A A 1111
A C 1112 A A 1155 A G 1156 A A 1157 A C 1158 A G
1160 A U 1183 A G 1184 A G 1185 A G 1186 A G 1187
A A 1188 A U 1189 A G 1190 A A 1227 A C 1228 A C
1230 A G 1231 A U 1232 A G 1233 A C 1342 A G 1343
A C 1366 A C 1367 A G 20 U A 21 U G 22 U A 23 U U
39 U C 40 U U 41 U C 27 V C 28 V A 29 V G 34 V A
35 V A 36 V A 44 V G 45 V G 46 V
15 1.63 1.63 146.4 -0.96 -0.70 11.1 80 7 2 2 1 0 1 0  G 929 A C 930 A C 931 A C 932 A G 933 A C 972 A G
973 A A 974 A A 975 A G 976 A C 995 A A 996 A G
1047 A G 1048 A U 1049 A G 1061 A U 1062 A U 1065
A C 1066 A G 1088 A G 1089 A U 1090 A U 1091 A A
1092 A A 1110 A U 1173 A G 1182 A U 1183 A G 1185
A G 1186 A G 1187 A A 1188 A U 1189 A G 1190 A U
1202 A C 1203 A A 1204 A U 1205 A C 1359 A C 1367
A A 1377 A C 1378 A U 1380 A C 1533 A
16 2.24 4.81 148.2 -0.86 -0.30 13.7 83 12 2 5 10 3 1 0  G 11 A U 12 A U 17 A C 18 A G 506 A C 507 A C
1071 A G 1072 A G 1079 A A 1080 A A 1105 A G 1106
A C 1107 A A 1110 A A 1111 A G 1156 A A 1157 A C
1158 A G 1160 A
17 2.24 4.81 151.7 -0.59 -0.49 10.1 78 5 3 2 7 2 1 0  G 505 A G 506 A C 528 A G 529 A G 530 A U 531 A A
532 A U 534 A A 949 A U 950 A U 952 A G 953 A G
954 A U 955 A U 956 A U 960 A U 961 A C 962 A G
963 A C 1051 A U 1052 A C 1054 A A 1055 A A 1196
A G 1222 A U 1224 A A 1225 A C 1226 A C 1320 A U
1321 A G 30 U A 31 U G 34 U A 35 U
18 1.92 1.93 155.2 -0.88 -0.66 8.8 72 7 2 0 1 2 3 0  C 948 A A 968 A U 1062 A U 1065 A C 1066 A A 1110
A A 1111 A C 1112 A A 1155 A G 1156 A A 1157 A C
1158 A G 1160 A U 1183 A G 1184 A G 1185 A G 1186
A G 1187 A A 1188 A U 1189 A G 1190 A G 1222 A U
1224 A A 1225 A C 1226 A G 1233 A C 1234 A U 1235
A U 1307 A U 1308 A C 1320 A U 1321 A C 1322 A G
1323 A A 1324 A C 1325 A C 1342 A G 1343 A A 1350
A U 1351 A C 1352 A G 1353 A U 1364 A G 1365 A C
1366 A C 1367 A
19 2.25 2.25 159.2 -0.88 -0.18 13.8 79 10 4 2 6 4 2 0  A 996 A G 1047 A G 1058 A U 1118 A C 1119 A C
1120 A U 1121 A U 1122 A U 1123 A G 1124 A A 1145
A A 1146 A A 1152 A G 1153 A A 1155 A G 1156 A G
1177 A G 1178 A A 1179 A C 1203 A A 1204 A
20 1.53 1.53 168.2 -0.51 -0.37 8.0 74 5 2 2 3 4 1 0  U 957 A A 958 A A 959 A U 960 A C 962 A G 963 A U
982 A A 983 A C 984 A C 985 A U 986 A A 994 A C
995 A G 1048 A U 1049 A G 1050 A C 1051 A C 1112
A C 1113 A C 1114 A A 1152 A G 1153 A G 1154 A A
1155 A G 1156 A A 1157 A C 1158 A G 1160 A U 1202
A C 1214 A G 1215 A A 1216 A G 30 U A 31 U
21 2.40 2.40 173.2 -1.10 -0.55 13.2 83 13 2 3 3 3 0 0  A 8 A G 9 A A 10 A G 11 A U 12 A U 17 A C 18 A A
26 A G 27 A A 28 A U 29 A U 30 A A 33 A C 34 A G
35 A C 36 A U 37 A G 38 A G 57 A C 58 A A 59 A G
61 A U 358 A G 359 A U 365 A A 366 A U 367 A U
368 A G 369 A C 370 A A 371 A C 372 A C 386 A U
387 A G 388 A C 396 A U 398 A G 399 A G 506 A C
507 A U 508 A A 509 A C 545 A G 548 A C 549 A G
550 A U 551 A C 1071 A G 1072 A G 1079 A A 1080 A
A 1105 A G 1106 A C 1107 A A 1110 A A 1111 A G
1156 A A 1157 A C 1158 A G 1160 A
22 1.63 1.63 174.2 -0.85 -0.75 8.4 76 6 2 1 0 1 1 0  G 929 A C 930 A C 931 A C 932 A G 933 A C 948 A A
968 A U 1062 A U 1065 A C 1066 A G 1088 A G 1089
A U 1090 A U 1091 A A 1092 A A 1110 A U 1173 A G
1182 A U 1183 A G 1185 A G 1186 A G 1187 A A 1188
A U 1189 A G 1190 A G 1222 A U 1224 A A 1225 A C
1226 A G 1233 A C 1234 A U 1235 A U 1307 A U 1308
A C 1320 A U 1321 A C 1322 A G 1323 A A 1324 A C
1325 A C 1342 A G 1343 A A 1350 A U 1351 A C 1352
A G 1353 A U 1364 A G 1365 A C 1366 A C 1367 A A
1377 A C 1378 A U 1380 A C 1533 A
23 1.97 1.97 179.0 -1.10 -0.71 11.2 81 11 2 2 0 1 1 0  C 932 A G 933 A C 948 A A 968 A U 1062 A U 1065 A
C 1066 A A 1067 A A 1092 A A 1093 A C 1096 A C
1097 A C 1098 A G 1099 A C 1100 A G 1104 A A 1105
A G 1106 A G 1108 A C 1109 A A 1110 A A 1171 A U
1183 A A 1188 A U 1189 A G 1190 A G 1222 A U 1224
A A 1225 A C 1226 A G 1233 A C 1234 A U 1235 A U
1307 A U 1308 A C 1320 A U 1321 A C 1322 A G 1323
A A 1324 A C 1325 A C 1342 A G 1343 A A 1350 A U
1351 A C 1352 A G 1353 A U 1364 A G 1365 A C 1366
A C 1367 A
24 2.54 2.68 204.2 -1.37 -0.65 15.8 85 17 3 6 5 2 0 0  U 827 A U 828 A G 829 A G 830 A A 831 A G 832 A G
833 A U 841 A C 848 A G 849 A U 850 A G 851 A G
859 A A 860 A G 861 A C 862 A C 1071 A G 1072 A U
1073 A G 1077 A U 1078 A G 1079 A A 1080 A A 1105
A G 1106 A C 1107 A A 1110 A A 1111 A G 1156 A A
1157 A C 1158 A G 1160 A
25 1.87 2.01 212.3 -1.17 -0.50 14.1 80 17 3 7 5 5 0 0  U 827 A U 828 A G 829 A G 830 A A 831 A G 832 A G
833 A U 841 A C 848 A G 849 A U 850 A G 851 A G
859 A A 860 A G 861 A C 862 A A 996 A G 1047 A G
1058 A C 1059 A U 1070 A C 1071 A G 1072 A U 1073
A G 1077 A U 1078 A G 1079 A A 1080 A G 1106 A C
1107 A A 1191 A C 1192 A G 1193 A C 1203 A A 1204
A U 1205 A
26 1.25 1.24 224.3 -1.26 -0.51 15.5 81 15 4 5 7 5 1 0  U 137 A G 138 A G 226 A G 227 A A 228 A U 229 A C
564 A U 565 A G 566 A C 599 A A 600 A G 601 A A
602 A U 603 A G 604 A U 605 A G 606 A G 628 A A
629 A A 630 A C 631 A U 632 A C 862 A C 1071 A G
1072 A U 1073 A G 1077 A U 1078 A G 1079 A A 1080
A A 1105 A G 1106 A C 1107 A A 1110 A A 1111 A G
1156 A A 1157 A C 1158 A G 1160 A
27 2.42 2.42 223.6 -0.69 -0.35 14.7 78 13 6 1 7 3 1 1  U 1118 A C 1119 A C 1120 A U 1121 A U 1122 A U
1123 A G 1124 A U 1125 A C 1141 A G 1142 A G 1143
A G 1144 A A 1145 A A 1146 A A 1155 A G 1156 A G
1177 A G 1178 A A 1179 A A 1256 A A 1257 A G 1258
A G 1272 A G 1278 A G 1279 A A 1280 A C 1281 A G
1312 A U 1313 A C 1314 A U 1315 A G 1316 A A 1360
A
28 2.62 2.63 229.6 -0.88 -0.72 9.0 79 9 1 2 1 0 2 0  G 670 A G 671 A U 672 A A 673 A G 693 A A 712 A G
713 A G 714 A A 715 A A 716 A U 717 A G 722 A U
723 A C 732 A G 733 A U 788 A U 789 A A 790 A C
805 A C 806 A G 926 A G 966 A C 967 A A 968 A A
969 A C 972 A G 973 A A 974 A A 975 A G 976 A C
995 A A 996 A G 1047 A G 1048 A U 1049 A G 1061 A
U 1202 A C 1203 A A 1204 A U 1205 A G 1231 A U
1232 A G 1233 A C 1342 A G 1343 A C 1359 A C 1366
A C 1367 A C 1400 A G 1401 A U 1498 A A 1503 A G
1505 A U 1506 A A 1507 A G 1525 A G 1526 A U 1527
A U 1528 A G 1530 A A 1531 A A 1534 A G 37 U A 38
U G 34 V A 35 V A 36 V G 37 V A 35 W
29 1.49 1.49 236.5 -0.86 -0.38 12.4 77 10 5 1 4 4 2 0  U 957 A A 958 A A 959 A U 960 A C 962 A G 963 A U
982 A A 983 A C 984 A C 985 A U 986 A A 994 A C
995 A G 1048 A U 1049 A G 1050 A C 1051 A U 1118
A C 1119 A C 1120 A U 1121 A U 1122 A U 1123 A G
1124 A A 1145 A A 1146 A A 1152 A G 1153 A A 1155
A G 1156 A G 1177 A G 1178 A A 1179 A U 1202 A C
1214 A G 1215 A A 1216 A G 30 U A 31 U
30 1.79 1.79 315.0 -0.72 -0.73 8.1 79 9 1 2 2 0 3 0  A 665 A G 693 A U 723 A G 724 A G 725 A C 726 A G
727 A A 729 A U 788 A U 789 A A 790 A G 818 A U
822 A C 823 A G 824 A A 825 A C 826 A G 829 A G
830 A A 831 A G 832 A G 833 A U 841 A C 848 A G
849 A U 850 A G 851 A G 852 A C 853 A U 854 A U
855 A U 870 A U 871 A G 926 A G 966 A C 967 A A
968 A A 969 A C 972 A G 973 A A 974 A A 975 A G
976 A C 995 A A 996 A U 997 A C 998 A C 999 A A
1000 A C 1001 A G 1002 A G 1003 A A 1004 A G 1033
A G 1034 A A 1035 A A 1036 A C 1037 A C 1038 A G
1039 A U 1049 A G 1061 A U 1202 A G 1231 A U 1232
A G 1233 A C 1342 A G 1343 A C 1359 A C 1366 A C
1367 A C 1400 A G 1401 A U 1498 A A 1503 A G 1505
A U 1506 A A 1507 A G 1526 A U 1527 A U 1528 A G
1530 A A 1531 A A 1534 A G 37 U A 38 U G 34 V A
35 V A 36 V G 37 V A 35 W

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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