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PDBsum entry 5mmj
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Top Page protein dna_rna metals Protein-protein interface(s) pores links
Pore analysis for: 5mmj calculated with MOLE 2.0 PDB id
5mmj
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 2.47 2.48 34.1 -1.88 -0.41 17.8 76 5 3 2 1 2 0 1  C 393 a C 1062 a A 1101 a C 1102 a C 1151 a A
1152 a
2 1.48 1.48 35.2 -0.49 -0.34 7.3 79 2 0 3 2 1 1 0  UNK 1057 8 G 780 a C 781 a C 794 a C 795 a C 796
a G 797 a MG 1642 a
3 1.40 1.40 43.9 -0.83 -0.65 11.0 86 2 0 0 1 0 0 0  UNK 1003 8 UNK 1005 8 UNK 1012 8 UNK 1013 8 UNK
1014 8 UNK 1015 8 UNK 1017 8 UNK 1019 8 UNK 1023
8 UNK 1025 8 UNK 1027 8 UNK 1029 8 UNK 1030 8 UNK
1032 8 UNK 1037 8 UNK 1038 8 UNK 1040 8 UNK 1044
8 UNK 1050 8 UNK 1052 8 UNK 1054 8 UNK 1057 8 UNK
1066 8 UNK 1068 8
4 2.37 2.37 49.3 -1.63 -0.72 17.5 81 3 2 2 0 0 0 0  C 393 a C 944 a A 945 a U 946 a C 948 a C 949 a A
984 a A 985 a C 986 a G 987 a C 988 a A 1152 a U
1153 a
5 2.61 2.61 58.6 -2.07 -0.47 23.9 79 7 2 4 2 0 1 0  C 393 a A 1152 a U 1153 a C 1205 a G 1206 a G
1208 a G 1264 a A 1308 a
6 1.48 1.48 62.6 -0.76 -0.40 11.5 85 6 0 3 2 1 0 0  C 671 a C 779 a G 780 a C 781 a C 794 a C 795 a U
805 a U 806 a G 1478 a A 1483 a C 1484 a MG 1642 a
7 1.21 1.21 80.6 -1.55 -0.55 18.4 75 5 2 1 2 2 0 0  UNK 1007 8 UNK 1008 8 UNK 1009 8 UNK 1010 8 UNK
1012 8 UNK 1013 8 UNK 1014 8 UNK 1015 8 UNK 1017
8 UNK 1027 8 UNK 1029 8 UNK 1030 8 UNK 1032 8 UNK
1037 8 UNK 1038 8 UNK 1040 8 UNK 1044 8 UNK 1045
8 UNK 1046 8 UNK 1050 8 UNK 1068 8 UNK 1245 8 UNK
1247 8 UNK 1251 8 UNK 1255 8 UNK 1256 8 UNK 1259
8 UNK 1260 8
8 1.59 1.59 83.6 -1.20 -0.48 15.0 76 4 1 1 4 1 1 0  UNK 1247 8 UNK 1251 8 UNK 1255 8 UNK 1256 8 UNK
1259 8 UNK 1260 8 C 1061 a C 1062 a C 1102 a A
1103 a G 1104 a A 1105 a
9 1.20 1.20 91.2 -1.21 -0.60 17.5 87 6 2 0 2 0 0 0  U 736 a U 737 a G 739 a A 740 a U 741 a A 742 a C
743 a G 875 a C 885 a A 886 a C 1327 a G 1328 a U
1330 a C 1331 a C 1332 a U 1444 a C 1445 a A 1448
a G 1454 a U 1455 a G 1466 a A 1467 a A 1468 a G
1469 a G 1470 a
10 1.21 1.21 91.2 -0.85 -0.74 9.3 86 4 0 0 1 0 0 0  C 883 a A 884 a C 885 a A 886 a C 916 a C 1012 a
U 1014 a C 1015 a A 1060 a C 1061 a C 1062 a G
1066 a C 1102 a A 1103 a G 1104 a A 1105 a C 1106
a U 1131 a G 1132 a A 1133 a G 1134 a G 1135 a U
1289 a C 1290 a G 1291 a C 1292 a C 1327 a G 1328
a U 1330 a C 1331 a C 1332 a C 1333 a G 1334 a MG
1620 a MG 1624 a
11 1.72 1.72 91.7 -0.40 -0.80 3.4 0 0 0 0 0 0 0 0  A 520 a A 521 a G 739 a A 740 a U 741 a A 742 a U
806 a C 815 a G 816 a G 836 a G 839 a G 866 a A
867 a A 868 a G 1341 a U 1342 a A 1343 a C 1353 a
G 1354 a U 1444 a C 1445 a A 1448 a A 1449 a U
1455 a G 1457 a C 1458 a C 1459 a G 1460 a U 1461
a G 1466 a A 1467 a A 1468 a G 1469 a G 1470 a U
1471 a G 1478 a G 1479 a A 1483 a MG 1535 a
12 1.46 1.46 97.1 -1.72 -0.53 20.0 82 8 4 3 3 2 0 0  UNK 1022 8 UNK 1024 8 UNK 1026 8 UNK 1057 8 UNK
1058 8 UNK 1059 8 UNK 1061 8 UNK 1062 8 UNK 1063
8 UNK 1064 8 UNK 1245 8 UNK 1247 8 UNK 1251 8 UNK
1255 8 UNK 1256 8 UNK 1259 8 UNK 1260 8 G 1048 a
C 1049 a U 1116 a
13 1.20 1.20 99.9 -0.87 -0.62 11.8 87 6 0 0 2 0 0 0  G 816 a U 869 a U 870 a G 871 a A 872 a C 873 a G
874 a G 875 a G 876 a G 877 a G 878 a C 879 a C
885 a A 886 a C 1327 a G 1328 a U 1330 a C 1331 a
C 1332 a G 1335 a G 1336 a C 1337 a C 1338 a U
1339 a U 1340 a G 1341 a U 1342 a G 1478 a A 1483
a MG 1572 a MG 1649 a
14 2.09 2.46 99.3 -0.75 -0.71 7.9 74 7 0 2 0 1 1 0  C 1061 a C 1062 a C 1063 a U 1064 a C 1065 a C
1077 a U 1084 a A 1086 a G 1099 a A 1101 a C 1102
a A 1103 a G 1104 a A 1196 a C 1197 a A 1198 a A
1199 a A 1200 a G 1201 a G 1206 a C 1207 a G 1208
a A 1209 a U 1210 a G 1218 a G 1219 a G 1220 a U
1221 a G 1222 a A 1228 a C 1229 a C 1230 a C 1232
a A 1233 a A 1234 a U 1263 a
15 2.92 2.92 123.5 -0.64 -0.59 7.9 79 5 1 0 3 1 1 0  C 15 a G 16 a A 17 a C 391 a A 392 a C 393 a U
460 a C 461 a G 475 a C 476 a A 480 a G 482 a A
483 a A 520 a A 521 a U 806 a C 815 a G 816 a G
835 a G 836 a A 864 a G 865 a G 866 a A 867 a A
868 a G 1154 a C 1155 a G 1341 a U 1342 a A 1343
a C 1346 a C 1352 a C 1353 a U 1439 a G 1440 a G
1478 a G 1479 a A 1483 a MG 1535 a MG 1591 a MG
1621 a
16 1.65 1.65 125.1 -1.30 -0.63 15.2 87 6 2 2 3 0 1 0  UNK 1022 8 UNK 1024 8 UNK 1026 8 UNK 1057 8 UNK
1058 8 UNK 1059 8 UNK 1061 8 UNK 1062 8 UNK 1063
8 UNK 1064 8 C 796 a G 1048 a C 1049 a C 1061 a C
1062 a C 1102 a A 1103 a G 1104 a A 1105 a C 1109
a C 1110 a U 1116 a A 1117 a A 1118 a
17 1.15 1.15 124.9 -1.39 -0.53 16.7 77 6 1 2 5 1 1 0  UNK 1007 8 UNK 1008 8 UNK 1009 8 UNK 1010 8 UNK
1012 8 UNK 1013 8 UNK 1014 8 UNK 1015 8 UNK 1017
8 UNK 1027 8 UNK 1029 8 UNK 1030 8 UNK 1032 8 UNK
1037 8 UNK 1038 8 UNK 1040 8 UNK 1044 8 UNK 1045
8 UNK 1046 8 UNK 1050 8 UNK 1068 8 UNK 1245 8 C
1061 a C 1062 a C 1102 a A 1103 a G 1104 a A 1105
a
18 1.86 1.86 133.6 -0.78 -0.64 8.4 80 4 1 0 3 1 1 0  C 15 a G 16 a A 17 a C 391 a A 392 a C 393 a U
460 a C 461 a G 475 a C 476 a A 480 a G 482 a A
483 a G 739 a A 740 a U 741 a A 742 a G 835 a G
836 a G 839 a A 864 a G 865 a G 1154 a C 1155 a A
1343 a C 1346 a C 1352 a C 1353 a G 1354 a U 1439
a G 1440 a U 1444 a C 1445 a A 1448 a A 1449 a U
1455 a G 1457 a C 1458 a C 1459 a G 1460 a U 1461
a G 1466 a A 1467 a A 1468 a G 1469 a G 1470 a U
1471 a MG 1591 a
19 2.26 2.37 135.6 -0.85 -0.70 9.0 74 6 1 2 1 1 1 0  G 613 a G 615 a C 616 a A 617 a G 618 a A 619 a G
620 a G 621 a G 622 a A 623 a A 624 a U 625 a U
626 a U 627 a G 639 a A 654 a U 655 a C 656 a G
657 a G 658 a A 659 a A 660 a A 661 a G 662 a A
663 a A 681 a U 683 a C 684 a U 685 a C 727 a G
728 a A 729 a U 731 a G 732 a G 733 a G 739 a A
740 a U 741 a A 742 a C 743 a C 745 a C 746 a G
748 a C 754 a G 792 a A 793 a U 1444 a C 1445 a G
1466 a MG 1583 a MG 1614 a MG 1659 a
20 1.29 1.29 133.2 -0.90 -0.61 11.5 79 11 0 1 1 2 0 0  C 885 a A 886 a C 889 a G 890 a G 891 a C 1182 a
U 1183 a A 1184 a C 1185 a G 1206 a C 1207 a G
1208 a G 1218 a G 1219 a G 1220 a U 1221 a G 1222
a C 1232 a C 1262 a U 1263 a C 1284 a G 1285 a U
1289 a C 1290 a U 1299 a C 1300 a G 1301 a C 1302
a C 1303 a G 1304 a G 1309 a C 1310 a A 1312 a U
1313 a A 1314 a C 1327 a G 1328 a U 1330 a C 1331
a
21 1.91 1.91 134.6 -0.62 -0.75 5.9 88 2 0 1 1 0 0 0  A 51 a C 53 a A 100 a G 101 a U 212 a G 213 a G
257 a U 258 a A 259 a U 288 a G 308 a A 309 a G
510 a A 520 a A 521 a A 522 a U 806 a C 815 a G
816 a U 833 a G 834 a G 835 a G 836 a G 837 a A
838 a G 839 a A 856 a A 857 a A 858 a G 866 a A
867 a A 868 a G 1341 a U 1342 a A 1343 a G 1372 a
C 1373 a G 1419 a C 1459 a G 1478 a G 1479 a A
1483 a MG 1535 a
22 1.46 1.46 135.5 -1.53 -0.59 16.4 80 6 3 4 2 3 0 0  UNK 1245 8 UNK 1247 8 UNK 1251 8 UNK 1255 8 UNK
1256 8 UNK 1259 8 UNK 1260 8 G 807 a U 808 a C
815 a G 816 a U 869 a C 1025 a G 1026 a G 1031 a
G 1048 a C 1049 a A 1050 a U 1116 a U 1340 a G
1341 a G 1478 a A 1483 a
23 1.20 1.20 139.9 -0.95 -0.38 16.1 85 12 2 0 6 1 0 0  C 391 a A 392 a C 393 a U 460 a C 461 a C 476 a A
480 a G 482 a A 483 a C 873 a G 874 a C 885 a A
886 a U 1142 a C 1143 a A 1144 a G 1154 a C 1155
a C 1327 a G 1328 a U 1330 a C 1331 a C 1332 a C
1333 a G 1334 a G 1335 a C 1346 a A 1347 a C 1348
a C 1349 a MG 1621 a
24 3.39 3.39 140.9 -0.82 -0.53 11.9 79 7 5 5 6 2 2 0  UNK 1102 8 UNK 1106 8 UNK 1110 8 G 807 a U 808 a
A 809 a G 810 a C 811 a U 812 a C 815 a G 816 a U
869 a G 1021 a U 1022 a C 1025 a G 1026 a U 1027
a G 1031 a A 1054 a G 1055 a A 1059 a A 1060 a C
1061 a C 1062 a C 1102 a A 1103 a G 1104 a U 1340
a G 1341 a G 1478 a A 1483 a
25 2.13 2.36 144.8 -0.98 -0.66 9.5 71 5 1 1 0 1 3 0  UNK 1057 8 G 613 a A 624 a U 625 a U 626 a G 639
a A 664 a C 665 a G 672 a G 673 a G 675 a A 677 a
G 679 a C 680 a C 727 a G 728 a A 729 a U 731 a G
732 a G 733 a G 739 a A 740 a U 741 a A 742 a C
743 a C 745 a C 746 a G 748 a G 766 a G 770 a A
771 a U 772 a A 773 a C 774 a G 777 a G 778 a C
779 a G 780 a C 781 a C 796 a G 797 a U 798 a G
799 a C 800 a A 801 a G 802 a U 803 a G 804 a U
819 a U 820 a A 821 a U 1444 a C 1445 a G 1466 a
MG 1583 a MG 1614 a
26 1.20 1.20 156.7 -0.98 -0.54 12.4 81 12 0 2 3 2 1 0  C 885 a A 886 a C 889 a G 890 a G 891 a A 898 a U
899 a G 1172 a A 1173 a C 1174 a C 1182 a U 1183
a A 1184 a C 1185 a C 1270 a C 1272 a C 1273 a C
1284 a G 1285 a U 1289 a C 1290 a U 1299 a C 1300
a G 1301 a C 1302 a C 1303 a G 1304 a C 1310 a C
1311 a A 1312 a U 1313 a A 1314 a C 1327 a G 1328
a U 1330 a C 1331 a MG 1547 a MG 1609 a
27 1.60 1.60 185.8 -0.94 -0.58 12.9 78 10 4 2 3 2 2 0  C 15 a G 16 a A 17 a G 475 a C 476 a G 739 a A
740 a U 741 a A 742 a G 835 a G 836 a G 839 a A
864 a G 865 a U 1019 a C 1020 a G 1021 a A 1054 a
G 1055 a A 1059 a A 1060 a C 1061 a C 1062 a C
1102 a A 1103 a G 1104 a C 1140 a G 1141 a U 1142
a C 1143 a A 1144 a A 1343 a C 1346 a C 1352 a C
1353 a G 1354 a U 1439 a G 1440 a U 1444 a C 1445
a A 1448 a A 1449 a U 1455 a G 1457 a C 1458 a C
1459 a G 1460 a U 1461 a G 1466 a A 1467 a A 1468
a G 1469 a G 1470 a U 1471 a MG 1591 a
28 2.61 2.88 187.1 -0.74 -0.66 8.5 79 7 0 1 2 1 1 0  UNK 1057 8 A 103 a A 104 a C 105 a G 209 a U 210
a C 211 a U 212 a U 223 a U 224 a A 229 a G 230 a
C 238 a U 239 a U 240 a C 248 a G 252 a A 253 a U
254 a C 255 a G 272 a G 273 a G 290 a G 291 a A
292 a U 513 a G 515 a G 516 a C 517 a G 580 a G
581 a G 770 a A 771 a U 772 a A 773 a C 774 a G
777 a G 778 a C 779 a G 780 a C 781 a C 796 a G
797 a U 798 a G 799 a C 800 a A 801 a G 802 a U
803 a U 819 a U 820 a A 821 a A 822 a G 823 a U
824 a A 825 a U 826 a C 827 a A 1375 a U 1376 a U
1385 a C 1386 a G 1387 a C 1414 a C 1415 a G 1416
a A 1417 a MG 1580 a
29 1.29 1.29 218.3 -0.87 -0.63 11.1 87 10 1 2 5 0 0 0  A 51 a C 53 a A 100 a G 101 a U 212 a G 213 a G
257 a U 258 a A 259 a U 288 a G 308 a A 309 a G
510 a A 521 a A 522 a U 833 a G 834 a G 835 a G
836 a G 837 a A 838 a G 839 a A 856 a A 857 a A
858 a G 875 a C 885 a A 886 a C 1327 a G 1328 a U
1330 a C 1331 a C 1332 a C 1353 a G 1354 a G 1372
a C 1373 a G 1419 a A 1452 a G 1454 a A 1456 a G
1457 a C 1458 a C 1459 a G 1460 a U 1461 a G 1469
a G 1470 a U 1471 a G 1472 a C 1473 a G 1479 a A
1480 a MG 1516 a
30 2.03 2.03 236.6 -0.91 -0.61 11.6 79 12 4 3 4 2 2 0  C 15 a G 16 a A 17 a A 51 a C 53 a A 100 a G 101
a U 212 a G 213 a G 257 a U 258 a A 259 a U 288 a
G 308 a A 309 a G 475 a C 476 a G 510 a A 521 a A
522 a U 833 a G 834 a G 835 a G 836 a G 837 a A
838 a G 839 a A 856 a A 857 a A 858 a A 864 a G
865 a G 866 a U 1019 a C 1020 a G 1021 a A 1054 a
G 1055 a A 1059 a A 1060 a C 1061 a C 1062 a C
1102 a A 1103 a G 1104 a C 1140 a G 1141 a U 1142
a C 1143 a A 1144 a A 1343 a C 1346 a C 1352 a C
1353 a G 1372 a C 1373 a G 1419 a U 1439 a G 1440
a C 1459 a MG 1535 a MG 1591 a

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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