spacer
spacer

PDBsum entry 3jam
Go to PDB code: 
Top Page protein dna_rna metals Protein-protein interface(s) pores links
Pore analysis for: 3jam calculated with MOLE 2.0 PDB id
3jam
Pores calculated on whole structure Pores calculated excluding ligands
View options
MOLEonline 2.0 manipulation
and
visualization
with HETATM:
without HETATM:
 
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 2.36 2.41 38.7 -1.18 -0.71 12.3 95 2 0 1 1 0 0 0  U 35 2 U 465 2 U 512 2 G 513 2 A 514 2 G 515 2 U
516 2 A 517 2 A 528 2 C 529 2 U 532 2 A 533 2 G
536 2 MG 201 J
2 2.18 2.65 85.0 -1.82 -0.39 24.1 86 10 2 3 5 0 1 0  A 533 2 G 676 2 G 677 2 G 765 2 C 777 2 G 778 2 A
780 2
3 2.39 2.39 91.7 -1.33 -0.66 16.2 85 7 2 3 2 0 0 0  U 35 2 C 36 2 U 37 2 C 38 2 A 39 2 U 462 2 A 463
2 G 464 2 U 465 2 U 516 2 U 523 2 A 528 2 G 676 2
G 677 2 G 765 2 U 766 2 U 767 2 G 772 2 G 775 2 G
776 2 C 777 2 MG 1837 2
4 2.31 2.43 103.5 -1.05 -0.59 13.6 82 6 4 3 4 0 2 0  U 240 2 U 241 2 G 242 2 A 243 2 A 252 2 G 647 2 U
648 2 U 649 2 U 678 2 U 679 2 C 687 2 G 688 2 G
689 2 G 703 2 C 704 2 A 734 2 C 735 2 A 737 2 G
738 2 U 750 2
5 1.55 1.66 108.4 -0.49 -0.49 6.0 77 3 0 2 3 3 1 0  G 34 2 U 35 2 C 36 2 U 37 2 C 38 2 A 39 2 U 60 2
A 61 2 A 72 2 U 73 2 U 74 2 U 75 2 G 81 2 U 82 2
G 83 2 A 270 2 A 444 2 A 445 2 C 454 2 A 455 2 U
462 2 A 463 2 G 464 2 U 465 2 U 516 2 U 523 2 A
528 2 G 775 2 MG 1837 2
6 1.72 2.01 113.9 -1.58 -0.34 19.2 83 10 6 8 4 4 2 1  G 1152 2 G 1153 2 U 1306 2 U 1796 2 U 1797 2 A
1798 2
7 1.39 1.39 120.9 -0.42 -0.79 3.3 58 0 0 0 0 0 1 0  G 34 2 U 35 2 C 36 2 U 37 2 C 38 2 A 39 2 A 40 2
A 41 2 G 42 2 A 43 2 U 44 2 U 45 2 A 46 2 A 47 2
G 48 2 C 97 2 U 98 2 C 99 2 A 100 2 U 101 2 A 409
2 A 424 2 C 426 2 A 427 2 A 437 2 G 460 2 G 461 2
U 462 2 A 463 2 G 464 2 U 465 2 G 466 2 U 516 2 A
528 2 G 1656 2 A 1657 2 A 1658 2 U 1659 2 G 1660
2 C 1731 2 U 1732 2 U 1733 2 G 1735 2 U 1736 2 C
1737 2 MG 1820 2 MG 1836 2 MG 1837 2
8 1.30 1.36 120.0 -1.08 -0.70 12.4 86 6 4 2 3 0 1 0  U 215 2 A 217 2 A 218 2 A 219 2 C 238 2 A 243 2 G
647 2 U 648 2 U 649 2 U 678 2 U 679 2 C 687 2 G
688 2 G 689 2 G 702 2 G 703 2 C 704 2 A 734 2 C
735 2 A 737 2 G 738 2 U 750 2
9 1.53 1.65 143.6 -1.06 -0.48 13.6 80 9 2 5 5 3 1 0  U 60 2 A 61 2 A 72 2 U 73 2 U 74 2 U 75 2 G 81 2
U 82 2 G 83 2 A 270 2 A 444 2 A 445 2 C 454 2 A
455 2 U 523 2 G 676 2 G 677 2 G 765 2 U 766 2 U
767 2 G 772 2 G 775 2 G 776 2 C 777 2
10 1.52 1.63 150.5 -1.00 -0.46 11.0 82 8 0 6 6 3 2 0  U 60 2 A 61 2 A 72 2 U 73 2 U 74 2 U 75 2 G 81 2
U 82 2 G 83 2 A 270 2 A 444 2 A 445 2 C 454 2 A
455 2 U 523 2 A 533 2 G 765 2 U 766 2 U 767 2 G
772 2 G 775 2 G 776 2 C 777 2 G 778 2 A 780 2
11 1.67 1.67 163.3 -0.69 -0.61 8.9 82 5 4 3 4 1 2 0  U 44 2 U 45 2 A 46 2 G 48 2 A 103 2 C 308 2 A 358
2 A 359 2 G 364 2 A 368 2 G 370 2 G 371 2 G 372 2
U 373 2 U 374 2 C 375 2 G 376 2 A 409 2 C 434 2 A
600 2 U 648 2 U 649 2 U 678 2 U 679 2 U 750 2 G
751 2 U 791 2 A 792 2 U 793 2 G 1656 2 A 1657 2 A
1658 2 U 1659 2 G 1660 2 C 1731 2 U 1732 2 U 1733
2 G 1735 2 U 1736 2 C 1737 2 U 1740 2 MG 1801 2
12 2.03 1.99 180.0 -0.78 -0.60 10.6 81 7 4 2 5 0 2 0  A 103 2 C 308 2 C 309 2 U 310 2 U 312 2 C 313 2 C
316 2 U 317 2 U 318 2 U 319 2 C 320 2 G 321 2 A
322 2 U 339 2 A 340 2 C 341 2 C 342 2 U 344 2 G
354 2 G 355 2 G 356 2 U 357 2 A 359 2 G 364 2 A
368 2 G 370 2 G 371 2 G 372 2 U 373 2 U 374 2 C
375 2 G 376 2 U 648 2 U 649 2 U 678 2 U 679 2 U
750 2 G 751 2 U 791 2 A 792 2 U 793 2 G 1117 2 C
1662 2 U 1663 2 U 1726 2 C 1727 2 A 1728 2 U 1736
2 C 1737 2 A 1738 2 U 1739 2 MG 1801 2
13 1.70 1.88 208.7 -1.28 -0.73 12.4 84 10 7 7 3 1 0 0  G 1152 2 G 1153 2 G 1154 2 C 1155 2 A 1156 2 C
1157 2 U 1284 2 U 1285 2 U 1306 2 G 1307 2 C 1308
2 U 1309 2 U 1310 2 A 1311 2 G 1329 2 A 1330 2 C
1332 2 U 1333 2 U 1334 2 A 1335 2 A 1336 2 C 1337
2 C 1338 2 A 1347 2 G 1348 2 G 1349 2 U 1378 2 U
1379 2 A 1380 2 G 1383 2 G 1385 2 U 1411 2 U 1412
2 U 1413 2 A 1415 2 G 1416 2 G 1478 2 C 1479 2 C
1480 2 G 1482 2 G 1519 2 C 1527 2 C 1528 2 G 1529
2 C 1613 2 G 1614 2 U 1615 2 C 1616 2 MG 1838 2
14 2.42 2.63 208.6 -1.48 -0.52 15.2 78 15 1 7 5 2 6 0  U 33 2 G 34 2 U 35 2 A 504 2 U 516 2 C 542 2 A
543 2 C 545 2 G 550 2 U 557 2 C 574 2 U 580 2 U
587 2 C 588 2 G 903 2 C 1147 2 G 1148 2 G 1149 2
A 1151 2 G 1152 2 G 1153 2 U 1190 2 U 1306 2 C
1424 2 A 1425 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 U 1796 2
15 1.35 2.57 218.5 -1.02 -0.40 12.3 82 8 8 10 13 6 5 0  U 1079 2 G 1152 2 G 1294 2 A 1295 2 U 1306 2 A
1318 2 U 1319 2 A 1320 2 A 1321 2 U 1396 2 C 1397
2
16 2.28 2.28 222.4 -0.59 -0.74 6.3 86 5 1 1 2 0 2 0  C 313 2 A 315 2 C 316 2 U 317 2 U 318 2 U 319 2 C
320 2 G 321 2 A 322 2 U 339 2 A 340 2 C 341 2 C
342 2 U 344 2 G 354 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 A 1029 2 G 1113 2 U 1119
2 C 1120 2 G 1126 2 C 1127 2 U 1128 2 G 1140 2 A
1141 2 A 1142 2 U 1143 2 U 1144 2 G 1152 2 U 1301
2 U 1302 2 U 1306 2 A 1321 2 U 1625 2 U 1626 2 G
1627 2 U 1628 2 A 1629 2 C 1662 2 U 1663 2 U 1726
2 C 1727 2 A 1728 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
17 2.18 2.18 245.9 -1.02 -0.62 10.3 77 9 1 5 2 2 2 0  A 46 2 G 48 2 A 358 2 A 409 2 G 903 2 U 998 2 C
999 2 A 1000 2 G 1149 2 G 1152 2 G 1153 2 U 1306
2 C 1635 2 G 1636 2 C 1637 2 C 1638 2 C 1639 2 G
1640 2 U 1641 2 C 1642 2 G 1643 2 C 1644 2 U 1645
2 A 1646 2 G 1647 2 U 1648 2 A 1649 2 C 1650 2 G
1656 2 A 1657 2 A 1658 2 U 1659 2 G 1660 2 C 1731
2 U 1732 2 U 1733 2 G 1735 2 U 1736 2 C 1737 2 U
1740 2 U 1741 2 A 1742 2 G 1743 2 A 1744 2 A 1747
2 A 1748 2 C 1749 2 U 1750 2 A 1751 2 A 1752 2 A
1753 2 A 1754 2 U 1759 2 G 1766 2 U 1796 2
18 1.65 2.34 247.9 -0.92 -0.67 11.8 84 8 3 4 4 1 0 0  C 313 2 A 315 2 C 316 2 U 317 2 G 354 2 G 355 2 A
880 2 U 881 2 C 882 2 A 883 2 G 884 2 U 885 2 A
886 2 A 918 2 U 919 2 U 920 2 G 921 2 A 922 2 A
923 2 G 924 2 A 925 2 G 971 2 A 972 2 A 973 2 C
974 2 G 984 2 U 1016 2 U 1017 2 A 1018 2 A 1019 2
C 1020 2 C 1021 2 U 1119 2 C 1120 2 G 1121 2 G
1656 2 A 1657 2 A 1658 2 U 1659 2 G 1660 2 G 1661
2 C 1662 2 U 1663 2 A 1729 2 A 1730 2 C 1731 2 U
1732 2 U 1733 2 G 1735 2 U 1736 2 C 1737 2
19 1.72 1.77 247.2 -0.97 -0.65 12.9 84 10 3 3 4 1 0 0  C 313 2 A 315 2 C 316 2 U 317 2 U 318 2 U 319 2 C
320 2 G 321 2 A 322 2 U 339 2 A 340 2 C 341 2 C
342 2 U 344 2 G 354 2 A 880 2 U 881 2 C 882 2 A
883 2 G 884 2 U 885 2 A 886 2 A 918 2 U 919 2 U
920 2 G 921 2 A 922 2 A 923 2 G 924 2 A 925 2 G
971 2 A 972 2 A 973 2 C 974 2 G 984 2 U 1016 2 U
1017 2 A 1018 2 A 1019 2 C 1020 2 C 1021 2 U 1119
2 C 1120 2 G 1121 2 C 1662 2 U 1663 2 U 1726 2 C
1727 2 A 1728 2 U 1736 2 C 1737 2
20 1.98 1.98 252.2 -1.53 -0.53 19.3 82 22 7 9 9 3 5 0  U 1 2 U 3 2 A 368 2 G 370 2 G 371 2 G 550 2 G 551
2 G 552 2 A 554 2 U 557 2 C 574 2 U 580 2 U 648 2
U 649 2 U 678 2 U 750 2 G 751 2 U 759 2 A 760 2 U
791 2 G 903 2 C 1147 2 G 1148 2 G 1149 2 A 1151 2
G 1152 2 G 1153 2 U 1190 2 U 1306 2 C 1424 2 A
1425 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 U 1796 2
21 1.27 1.81 314.8 -1.34 -0.51 14.9 82 18 14 14 13 5 3 0  C 1332 2 U 1333 2 U 1334 2 A 1335 2 A 1336 2 C
1337 2 C 1338 2 A 1347 2 G 1348 2 G 1349 2 U 1378
2 U 1379 2 A 1380 2 A 1382 2 G 1383 2 G 1384 2 G
1385 2 G 1478 2 C 1479 2 C 1480 2 G 1482 2 G 1519
2 C 1527 2 C 1528 2 G 1529 2
22 1.30 1.36 309.2 -1.00 -0.60 10.7 81 12 4 10 9 5 4 0  U 215 2 A 216 2 A 217 2 A 218 2 A 219 2 C 238 2 A
246 2 G 702 2 G 703 2 G 738 2 G 739 2 A 740 2 C
741 2 U 742 2 G 808 2 G 809 2 A 810 2 A 816 2 G
845 2 A 846 2 C 847 2 C 869 2 G 870 2 G 871 2 C
873 2 G 875 2 G 877 2 G 878 2 C 879 2 A 880 2 U
881 2 C 882 2 A 883 2 G 884 2 U 885 2 A 886 2 A
918 2 U 919 2 U 920 2 G 921 2 A 922 2 A 923 2 G
924 2 A 925 2 A 943 2 U 944 2 U 946 2 C 948 2 C
949 2 A 950 2 A 951 2 G 952 2 U 1016 2
23 1.58 1.71 310.4 -1.62 -0.64 15.3 82 22 11 17 7 4 5 0  U 33 2 G 34 2 U 35 2 A 504 2 U 516 2 C 542 2 A
543 2 C 545 2 G 550 2 U 557 2 C 574 2 U 580 2 U
587 2 C 588 2 G 1276 2 G 1277 2 C 1278 2 C 1279 2
C 1332 2 U 1333 2 U 1334 2 A 1335 2 A 1336 2 C
1337 2 C 1338 2 A 1347 2 G 1348 2 G 1349 2 U 1378
2 U 1379 2 A 1380 2 A 1382 2 G 1383 2 A 1419 2 A
1420 2 A 1423 2 C 1424 2 G 1478 2 C 1479 2 C 1480
2 G 1482 2 G 1519 2 C 1527 2 C 1528 2 G 1529 2
24 1.65 1.82 310.6 -1.02 -0.60 11.0 84 13 6 10 8 4 4 0  G 647 2 U 648 2 U 649 2 U 678 2 C 687 2 G 688 2 G
689 2 A 690 2 U 698 2 A 733 2 C 735 2 C 736 2 U
742 2 U 744 2 U 745 2 A 746 2 U 750 2 C 797 2 A
798 2 U 799 2 G 800 2 A 802 2 U 807 2 G 808 2 C
869 2 G 870 2 G 871 2 C 873 2 G 875 2 G 877 2 G
878 2 C 879 2 A 880 2 U 881 2 C 882 2 A 883 2 G
884 2 U 885 2 A 886 2 A 918 2 U 919 2 U 920 2 G
921 2 A 922 2 A 923 2 G 924 2 A 925 2 A 943 2 U
944 2 U 946 2 C 948 2 C 949 2 A 950 2 A 951 2 G
952 2 U 1016 2
25 1.29 2.20 317.7 -1.32 -0.40 17.0 78 17 15 13 15 9 8 0  U 33 2 G 34 2 U 35 2 A 504 2 U 516 2 C 542 2 A
543 2 C 545 2 U 587 2 C 588 2 G 1290 2 G 1291 2 G
1323 2 A 1324 2 A 1325 2
26 1.61 1.72 354.0 -1.60 -0.61 17.5 83 29 17 19 11 6 4 0  U 1 2 U 3 2 A 368 2 G 370 2 G 371 2 G 550 2 G 551
2 G 552 2 A 554 2 U 557 2 C 574 2 U 580 2 U 648 2
U 649 2 U 678 2 U 750 2 G 751 2 U 759 2 A 760 2 U
791 2 G 1276 2 G 1277 2 C 1278 2 C 1279 2 C 1332
2 U 1333 2 U 1334 2 A 1335 2 A 1336 2 C 1337 2 C
1338 2 A 1347 2 G 1348 2 G 1349 2 U 1378 2 U 1379
2 A 1380 2 A 1382 2 G 1383 2 A 1419 2 A 1420 2 A
1423 2 C 1424 2 G 1478 2 C 1479 2 C 1480 2 G 1482
2 G 1519 2 C 1527 2 C 1528 2 G 1529 2
27 1.45 1.45 359.0 -1.32 -0.71 11.7 83 17 11 15 3 4 2 0  U 9 2 G 10 2 A 46 2 G 48 2 A 358 2 A 409 2 G 573
2 C 574 2 A 1138 2 G 1276 2 G 1277 2 C 1278 2 C
1279 2 C 1332 2 U 1333 2 U 1334 2 A 1335 2 A 1336
2 C 1337 2 C 1338 2 A 1347 2 G 1348 2 G 1349 2 U
1378 2 U 1379 2 A 1380 2 A 1382 2 G 1383 2 A 1419
2 A 1420 2 A 1423 2 C 1424 2 G 1478 2 C 1479 2 C
1480 2 G 1482 2 G 1519 2 C 1527 2 C 1528 2 G 1529
2 C 1632 2 C 1638 2 C 1639 2 G 1640 2 U 1641 2 C
1642 2 G 1643 2 C 1644 2 U 1645 2 A 1646 2 G 1647
2 U 1648 2 A 1649 2 C 1650 2 G 1656 2 A 1657 2 A
1658 2 U 1659 2 G 1660 2 C 1731 2 U 1732 2 U 1733
2 G 1735 2 U 1736 2 C 1737 2 U 1740 2 U 1741 2 A
1742 2 G 1743 2 A 1744 2 A 1747 2 A 1748 2 C 1749
2 U 1750 2 A 1751 2 A 1752 2 A 1753 2 MG 1810 2
28 1.27 2.61 365.5 -1.46 -0.43 20.3 82 22 23 14 21 7 7 0  U 1 2 U 3 2 A 368 2 G 370 2 G 371 2 U 648 2 U 649
2 U 678 2 U 750 2 G 751 2 U 759 2 A 760 2 U 791 2
G 1290 2 G 1291 2 G 1323 2 A 1324 2 A 1325 2
29 1.62 1.75 410.2 -1.20 -0.70 11.3 83 18 11 14 4 4 2 0  U 9 2 G 10 2 C 313 2 A 315 2 C 316 2 U 317 2 U
318 2 U 319 2 C 320 2 G 321 2 A 322 2 U 339 2 A
340 2 C 341 2 C 342 2 U 344 2 G 354 2 G 573 2 C
574 2 A 618 2 A 619 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 A 1029 2 G 1110 2 G 1113 2 U 1119
2 C 1120 2 G 1126 2 C 1127 2 U 1128 2 A 1138 2 G
1139 2 G 1140 2 G 1276 2 G 1277 2 C 1278 2 C 1279
2 C 1332 2 U 1333 2 U 1334 2 A 1335 2 A 1336 2 C
1337 2 C 1338 2 A 1347 2 G 1348 2 G 1349 2 U 1378
2 U 1379 2 A 1380 2 A 1382 2 G 1383 2 A 1419 2 A
1420 2 A 1423 2 C 1424 2 G 1478 2 C 1479 2 C 1480
2 G 1482 2 G 1519 2 C 1527 2 C 1528 2 G 1529 2 A
1629 2 C 1632 2 C 1638 2 C 1639 2 C 1662 2 U 1663
2 U 1726 2 C 1727 2 A 1728 2 U 1736 2 C 1737 2 A
1751 2 A 1752 2 C 1771 2 G 1772 2 MG 1805 2 MG
1810 2 MG 1825 2
30 1.19 1.83 395.5 -1.07 -0.50 13.1 79 13 15 14 14 9 7 0  U 9 2 G 10 2 A 11 2 A 46 2 G 48 2 A 358 2 A 409 2
G 573 2 C 574 2 A 1138 2 G 1290 2 G 1291 2 G 1323
2 A 1324 2 A 1325 2 C 1632 2 C 1638 2 C 1639 2 G
1640 2 U 1641 2 C 1642 2 G 1643 2 C 1644 2 U 1645
2 A 1646 2 G 1647 2 U 1648 2 A 1649 2 C 1650 2 G
1656 2 A 1657 2 A 1658 2 U 1659 2 G 1660 2 C 1731
2 U 1732 2 U 1733 2 G 1735 2 U 1736 2 C 1737 2 U
1740 2 U 1741 2 A 1742 2 G 1743 2 A 1744 2 A 1747
2 A 1748 2 C 1749 2 U 1750 2 A 1751 2 A 1752 2 A
1753 2 MG 1810 2

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.
spacer
spacer