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PDBsum entry 1ibm
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Top Page protein dna_rna metals Protein-protein interface(s) pores links
Pore analysis for: 1ibm calculated with MOLE 2.0 PDB id
1ibm
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 3.06 3.06 30.0 -0.40 -0.80 3.4 0 0 0 0 0 0 0 0  G 61 A U 62 A C 63 A G 64 A U 65 A C 67 A G 68 A
G 93 A U 95 A G 96 A G 97 A U 98 A C 99 A A 101 A
A 143 A G 144 A G 145 A G 146 A A 172 A U 173 A G
198 A G 199 A G 200 A C 385 A
2 3.23 3.43 45.3 -0.67 -0.48 11.1 75 3 0 1 2 0 0 0  C 58 A G 61 A C 99 A A 101 A G 102 A A 151 A A
152 A C 163 A U 164 A C 165 A G 1435 A G 1461 A
3 3.31 3.31 47.6 -0.45 -0.67 8.6 78 0 1 0 1 1 0 0  C 590 A C 600 A C 601 A G 638 A G 639 A A 640 A U
641 A A 642 A C 651 A U 652 A A 653 A G 654 A C
748 A C 826 A U 827 A G 829 A G 830 A U 831 A U
833 A C 834 A U 835 A C 840 A C 848 A C 849 A U
850 A G 851 A U 870 A
4 1.40 1.40 65.7 -0.95 -0.50 16.5 76 6 1 0 3 0 0 0  A 143 A G 144 A G 145 A G 146 A C 176 A C 177 A C
178 A A 195 A A 196 A A 197 A G 198 A G 199 A G
1441 A G 1442 A A 1451 A C 1452 A G 1453 A G 1454
A
5 2.19 2.19 75.4 -0.37 -0.65 6.1 73 0 0 0 0 0 0 0  U 5 A A 50 A A 119 A G 238 A U 239 A C 240 A U
287 A A 288 A C 290 A C 291 A G 292 A G 293 A U
294 A G 297 A G 299 A A 300 A G 301 A G 302 A A
303 A U 304 A G 361 A G 362 A C 555 A G 630 A G
631 A
6 2.07 2.10 78.1 -0.63 -0.77 6.4 83 3 1 2 1 0 0 0  C 25 A A 26 A A 50 A U 287 A A 288 A G 361 A G
362 A G 416 A G 428 A G 500 A C 501 A G 502 A C
503 A C 504 A C 508 A C 522 A A 523 A G 524 A C
536 A G 537 A G 540 A G 541 A G 542 A U 551 A U
552 A C 554 A C 555 A G 557 A MG 1601 A
7 2.19 2.19 82.1 -0.40 -0.73 4.7 68 1 0 0 1 0 0 0  A 50 A G 52 A G 117 A U 118 A A 119 A A 120 A G
122 A C 233 A U 252 A G 258 A G 259 A G 260 A G
265 A C 267 A C 268 A C 269 A G 286 A U 287 A C
314 A G 318 A G 319 A C 320 A A 321 A C 328 A G
361 A G 362 A G 1423 A C 1424 A U 1425 A C 1426 A
U 1436 A C 1437 A G 1438 A C 1439 A C 1440 A G
1441 A G 1442 A G 1443 A G 1453 A G 1454 A
8 2.19 2.19 88.8 -0.40 -0.74 4.5 68 1 0 0 1 0 0 0  A 50 A G 52 A G 117 A U 118 A A 119 A A 120 A G
122 A U 164 A C 165 A C 233 A U 252 A C 267 A C
268 A G 286 A U 287 A C 314 A A 315 A G 316 A G
318 A G 319 A C 320 A C 328 A A 329 A G 333 A C
334 A C 335 A G 348 A A 349 A G 350 A G 351 A G
361 A G 362 A G 1423 A C 1424 A U 1425 A C 1426 A
G 1435 A G 1461 A MG 1635 A
9 2.07 2.10 90.9 -1.08 -0.78 11.6 83 0 0 0 0 0 0 0  U 5 A G 6 A A 26 A G 27 A G 28 A G 29 A U 296 A G
297 A G 299 A A 300 A G 416 A G 428 A G 500 A C
501 A G 502 A C 503 A C 504 A C 508 A A 509 A C
522 A A 523 A G 524 A C 536 A G 537 A G 540 A G
541 A G 542 A G 544 A C 545 A G 550 A U 551 A A
611 A C 612 A G 630 A MG 1601 A
10 1.72 1.72 97.5 -0.54 -0.78 5.2 72 1 0 0 0 0 0 0  U 5 A G 6 A G 29 A U 30 A G 44 A U 45 A C 58 A A
59 A G 61 A U 62 A C 99 A A 101 A C 295 A U 296 A
G 297 A G 299 A A 300 A G 306 A C 307 A C 308 A C
355 A A 356 A C 369 A C 370 A G 371 A C 372 A C
386 A U 387 A G 388 A C 390 A G 391 A G 392 A A
393 A C 400 A A 611 A C 612 A C 623 A C 624 A G
630 A
11 2.79 3.02 100.8 -1.28 -0.76 15.0 76 0 0 0 0 0 0 0  U 5 A G 299 A A 300 A U 565 A G 566 A G 567 A G
568 A C 569 A G 630 A G 821 A C 822 A G 823 A C
824 A G 825 A C 826 A G 829 A G 830 A U 831 A U
833 A C 834 A U 835 A C 840 A C 848 A C 849 A U
850 A G 851 A G 852 A U 870 A U 871 A A 872 A A
873 A G 874 A C 875 A G 876 A C 877 A
12 2.33 2.33 103.5 -0.63 -0.70 6.8 67 2 1 0 1 1 0 0  A 50 A C 242 A A 243 A U 244 A G 286 A U 287 A A
288 A G 361 A G 362 A A 759 A G 760 A G 761 A C
762 A G 763 A C 764 A G 765 A G 769 A C 770 A G
771 A U 772 A G 773 A U 801 A A 802 A G 803 A U
804 A C 805 A C 806 A A 807 A C 808 A G 809 A C
810 A C 811 A C 812 A C 882 A G 895 A C 896 A C
897 A G 903 A C 904 A U 905 A G 906 A A 907 A A
908 A C 1479 A MG 1552 A MG 1553 A
13 3.27 3.27 109.7 -0.64 -0.72 7.1 71 4 0 0 1 0 1 0  U 5 A U 118 A A 119 A A 120 A C 121 A G 122 A C
233 A G 238 A U 239 A C 240 A U 252 A U 253 A G
258 A G 259 A G 260 A G 265 A C 267 A C 268 A C
269 A C 277 A G 281 A A 282 A C 283 A G 292 A G
293 A G 297 A G 299 A A 300 A G 301 A G 302 A C
314 A G 319 A C 320 A A 321 A C 328 A G 630 A G
631 A A 632 A U 1436 A C 1437 A G 1438 A C 1439 A
C 1440 A G 1441 A G 1442 A G 1443 A G 1453 A G
1454 A MG 1607 A
14 2.36 2.36 116.6 -1.31 -0.39 20.4 78 11 2 1 4 1 1 0  G 587 A C 589 A C 590 A U 591 A G 592 A C 600 A C
601 A G 638 A G 639 A A 640 A U 641 A A 642 A C
643 A G 644 A C 645 A U 646 A C 647 A G 649 A C
754 A G 763 A C 764 A G 765 A G 769 A C 770 A G
771 A U 772 A G 773 A U 801 A A 802 A G 803 A U
804 A C 805 A C 806 A A 807 A C 808 A G 809 A C
810 A C 811 A MG 1552 A MG 1553 A
15 2.65 2.65 116.4 -0.61 -0.73 6.7 71 4 0 0 1 0 1 0  U 5 A U 118 A A 119 A A 120 A C 121 A G 122 A U
164 A C 165 A C 233 A G 238 A U 239 A C 240 A U
252 A U 253 A C 267 A C 268 A C 277 A G 281 A A
282 A C 283 A G 292 A G 293 A G 297 A G 299 A A
300 A G 301 A G 302 A C 314 A A 315 A G 316 A G
318 A G 319 A C 320 A C 328 A A 329 A G 333 A C
334 A C 335 A G 348 A A 349 A G 350 A G 351 A G
630 A G 631 A A 632 A G 1435 A G 1461 A MG 1607 A
MG 1635 A
16 2.34 2.34 119.6 -0.47 -0.72 5.4 68 0 0 0 0 0 0 0  U 5 A G 238 A U 239 A C 240 A C 241 A C 242 A A
243 A U 244 A G 281 A G 292 A G 293 A G 297 A G
299 A A 300 A G 301 A G 302 A G 630 A G 631 A A
632 A A 759 A G 760 A G 761 A C 762 A G 763 A C
764 A G 765 A G 769 A C 770 A G 771 A U 772 A G
773 A U 801 A A 802 A G 803 A U 804 A C 805 A C
806 A A 807 A C 808 A G 809 A C 810 A C 811 A C
812 A G 895 A C 896 A C 897 A G 903 A C 904 A U
905 A MG 1552 A MG 1553 A
17 1.56 1.56 124.6 -0.58 -0.71 7.0 74 4 0 0 1 0 0 0  A 50 A G 52 A G 117 A U 118 A A 119 A A 120 A G
122 A U 133 A A 134 A A 143 A G 144 A G 145 A G
146 A U 173 A C 175 A C 176 A A 196 A A 197 A G
198 A G 199 A U 222 A C 233 A U 252 A U 261 A A
262 A A 263 A G 265 A C 267 A C 268 A G 286 A U
287 A C 314 A G 318 A G 319 A C 320 A C 322 A G
324 A A 325 A G 326 A A 327 A C 328 A G 361 A G
362 A G 1423 A C 1424 A U 1425 A C 1426 A MG 1577
A MG 1608 A
18 2.79 2.96 124.8 -1.30 -0.76 14.3 75 0 0 0 0 0 0 0  U 5 A MG 71 A G 299 A A 300 A U 565 A G 566 A G
630 A G 858 A A 859 A A 860 A G 861 A C 862 A U
863 A C 866 A G 867 A U 920 A U 921 A G 922 A A
923 A C 924 A G 925 A G 926 A C 1076 A G 1077 A U
1078 A G 1082 A C 1384 A G 1385 A G 1386 A G 1387
A C 1388 A C 1389 A U 1390 A U 1391 A C 1400 A MG
1644 A C 5 X
19 3.22 3.22 125.6 -0.52 -0.69 6.2 66 1 1 0 1 1 0 0  A 50 A U 287 A A 288 A G 361 A G 362 A G 966 A C
1195 A U 1196 A C 1384 A G 1385 A G 1386 A C 1397
A A 1398 A C 1399 A C 1400 A C 1403 A C 1404 A G
1405 A U 1406 A C 1407 A A 1408 A C 1409 A G 1410
A C 1411 A C 1412 A A 1413 A U 1414 A C 1479 A G
1480 A U 1481 A G 1482 A A 1483 A U 1485 A G 1487
A G 1488 A G 1489 A C 1490 A G 1491 A G 1494 A U
1495 A MG 1624 A MG 1649 A MG 1650 A MG 1653 A C
5 X U 6 X A 38 Y U 1 Z U 2 Z U 4 Z
20 1.82 1.82 140.9 -0.83 -0.78 8.1 83 5 3 2 0 0 0 0  A 26 A G 27 A G 28 A G 29 A U 30 A G 44 A U 45 A
C 58 A A 59 A G 61 A U 62 A C 99 A A 101 A C 295
A G 306 A C 307 A C 308 A C 355 A A 356 A C 369 A
C 370 A G 371 A C 372 A C 386 A U 387 A G 388 A C
390 A G 391 A G 392 A A 393 A C 400 A G 416 A G
428 A G 500 A C 501 A G 502 A C 503 A C 504 A C
508 A A 509 A C 522 A A 523 A G 524 A C 536 A G
537 A G 540 A G 541 A G 542 A G 544 A C 545 A G
550 A U 551 A C 623 A C 624 A MG 1601 A
21 1.57 1.57 151.2 -0.48 -0.59 7.7 77 4 1 0 3 0 1 0  G 128 A U 129 A G 129 A i:A C 132 A U 133 A A 134
A A 143 A G 144 A G 145 A G 146 A U 173 A C 175 A
C 176 A G 190 A i:G U 190 A i:D C 190 A i:C G 190
A i:H U 190 A i:E A 196 A A 197 A G 198 A G 199 A
MG 210 A U 222 A U 223 A C 224 A C 225 A G 226 A
G 227 A A 300 A A 325 A C 596 A G 597 A C 600 A C
601 A A 602 A U 603 A G 630 A G 631 A A 632 A G
633 A C 634 A G 635 A U 636 A G 637 A G 638 A MG
1608 A MG 1621 A
22 2.35 2.35 153.2 -0.61 -0.78 6.1 74 4 0 0 0 0 0 0  U 118 A A 119 A A 120 A C 121 A G 122 A U 164 A C
165 A C 233 A U 239 A C 240 A C 241 A C 242 A A
243 A U 244 A U 252 A U 253 A C 267 A C 268 A C
277 A G 281 A A 282 A C 283 A C 314 A A 315 A G
316 A G 318 A G 319 A C 320 A C 328 A A 329 A G
333 A C 334 A C 335 A G 348 A A 349 A G 350 A G
351 A A 759 A G 760 A G 761 A C 762 A G 763 A C
764 A G 765 A G 769 A C 770 A G 771 A U 772 A G
773 A U 801 A A 802 A G 803 A U 804 A C 805 A C
806 A A 807 A C 808 A G 809 A C 810 A C 811 A C
812 A G 895 A C 896 A C 897 A G 903 A C 904 A U
905 A G 1435 A G 1461 A MG 1552 A MG 1553 A MG
1607 A MG 1635 A
23 2.76 2.92 170.6 -1.07 -0.53 12.7 81 0 0 0 0 0 0 0  U 5 A G 299 A A 300 A U 565 A G 566 A G 567 A G
568 A C 569 A G 630 A A 665 A G 693 A G 718 A C
719 A A 722 A U 723 A G 724 A G 725 A C 726 A G
727 A A 729 A C 732 A A 733 A G 818 A G 821 A C
822 A G 823 A C 824 A G 854 A G 855 A U 871 A A
872 A A 873 A G 874 A C 875 A G 876 A C 877 A C
1527 A A 1534 A
24 1.53 1.53 206.3 -0.56 -0.54 10.2 80 9 4 0 6 0 1 0  G 128 A U 129 A G 129 A i:A C 132 A U 133 A A 134
A A 143 A G 144 A G 145 A G 146 A U 173 A C 175 A
C 176 A G 190 A i:G U 190 A i:D C 190 A i:C G 190
A i:H U 190 A i:E A 196 A A 197 A G 198 A G 199 A
U 222 A U 223 A C 224 A C 225 A G 226 A G 227 A A
325 A G 587 A C 589 A C 590 A U 591 A G 592 A G
594 A C 596 A C 600 A C 601 A G 637 A G 639 A A
640 A U 641 A A 642 A C 643 A G 644 A C 645 A U
646 A C 647 A G 649 A C 754 A MG 1608 A
25 1.63 1.63 219.1 -0.76 -0.42 14.3 80 15 4 1 11 1 2 0  G 128 A U 129 A G 129 A i:A C 132 A U 133 A A 134
A A 143 A G 144 A G 145 A G 146 A U 173 A C 175 A
C 176 A G 190 A i:G U 190 A i:D C 190 A i:C G 190
A i:H U 190 A i:E A 196 A A 197 A G 198 A G 199 A
U 222 A U 223 A C 224 A C 225 A G 226 A G 227 A A
325 A G 594 A C 596 A G 637 A U 646 A C 647 A G
763 A C 764 A G 765 A G 769 A C 770 A G 771 A U
772 A G 773 A U 801 A A 802 A G 803 A U 804 A C
805 A C 806 A A 807 A C 808 A G 809 A C 810 A C
811 A MG 1552 A MG 1553 A MG 1608 A
26 1.89 1.92 215.3 -1.02 -0.65 13.1 84 0 0 0 0 0 0 0  U 5 A G 6 A A 8 A G 9 A A 10 A G 11 A A 26 A G 27
A G 297 A A 298 A G 299 A A 300 A U 421 A C 422 A
G 505 A G 506 A C 507 A C 508 A U 512 A C 513 A C
514 A A 532 A U 534 A G 557 A A 611 A C 612 A G
630 A G 993 A C 995 A A 996 A U 997 A G 998 A C
999 A U 1000 A A 1001 A G 1003 A i:A A 1004 A G
1032 A G 1033 A G 1034 A A 1035 A G 1036 A C 1037
A C 1038 A C 1045 A A 1046 A G 1047 A A 1204 A U
1205 A G 1206 A G 1207 A C 1208 A
27 1.54 1.54 224.8 -0.63 -0.57 9.8 77 8 2 0 5 1 3 0  G 129 A i:A U 129 A C 132 A U 133 A A 134 A A 143
A G 144 A G 145 A G 146 A U 173 A C 175 A C 176 A
G 190 A i:G U 190 A i:D C 190 A i:C U 190 A i:E G
190 A i:H A 196 A A 197 A G 198 A G 199 A U 222 A
U 223 A C 224 A C 225 A G 226 A G 227 A C 237 A A
325 A C 564 A U 565 A G 567 A G 568 A C 569 A C
596 A G 597 A G 633 A C 634 A G 635 A U 636 A G
637 A G 821 A C 822 A G 823 A C 824 A G 825 A C
826 A G 829 A G 830 A U 831 A U 833 A C 834 A U
835 A C 840 A C 848 A C 849 A U 850 A G 851 A G
852 A U 870 A U 871 A A 872 A A 873 A G 874 A G
876 A C 877 A MG 1608 A MG 1610 A MG 213 H
28 1.45 1.45 236.9 -1.03 -0.61 12.1 77 14 2 1 6 3 1 0  U 5 A G 6 A A 8 A G 9 A A 10 A G 11 A A 26 A G 27
A G 297 A A 298 A G 299 A A 300 A G 505 A G 506 A
C 507 A C 508 A C 528 A U 534 A G 557 A C 600 A C
601 A A 602 A A 611 A C 612 A G 630 A G 631 A G
638 A G 639 A U 950 A G 953 A G 954 A U 955 A U
960 A C 962 A G 963 A A 964 A A 965 A G 966 A C
1195 A U 1196 A G 1224 A A 1225 A C 1226 A C 1322
A C 1397 A U 32 Y U 33 Y G 34 Y U 1 Z U 2 Z U 4 Z
29 2.43 2.43 253.4 -0.91 -0.68 10.5 80 9 1 1 3 1 0 0  U 14 A G 15 A A 16 A A 50 A U 287 A A 288 A G 361
A G 362 A U 421 A C 422 A U 512 A C 513 A C 514 A
G 527 A C 528 A A 532 A U 534 A G 993 A C 995 A A
996 A U 997 A G 998 A C 999 A U 1000 A A 1001 A G
1003 A i:A A 1004 A G 1032 A G 1033 A G 1034 A A
1035 A G 1036 A C 1037 A C 1038 A C 1045 A A 1046
A G 1047 A A 1204 A U 1205 A G 1206 A G 1207 A C
1208 A C 1403 A C 1404 A G 1405 A U 1406 A C 1407
A A 1408 A C 1409 A G 1410 A C 1411 A C 1412 A A
1413 A U 1414 A C 1479 A G 1480 A U 1481 A G 1482
A A 1483 A U 1485 A G 1487 A G 1488 A G 1489 A C
1490 A G 1491 A A 1492 A MG 1559 A MG 1649 A MG
1650 A MG 1653 A U 3 Z U 4 Z
30 1.52 1.52 265.8 -0.74 -0.69 7.8 68 6 1 0 2 3 1 0  C 58 A A 59 A G 61 A C 99 A A 101 A G 117 A U 118
A A 119 A A 120 A G 122 A C 233 A U 252 A C 267 A
C 268 A G 284 A G 286 A U 287 A C 314 A A 315 A G
316 A G 318 A G 319 A C 320 A C 328 A A 329 A C
330 A G 331 A G 332 A G 333 A G 350 A G 351 A U
950 A G 953 A G 954 A U 955 A U 960 A C 962 A G
963 A A 964 A A 965 A G 966 A U 1196 A G 1224 A A
1225 A C 1226 A C 1322 A C 1400 A C 1403 A C 1404
A G 1405 A U 1406 A C 1407 A A 1408 A C 1409 A G
1410 A C 1411 A C 1412 A A 1413 A U 1414 A G 1423
A C 1424 A U 1425 A C 1426 A C 1478 A C 1479 A G
1480 A U 1481 A G 1482 A A 1483 A U 1485 A G 1487
A G 1488 A G 1489 A C 1490 A G 1491 A G 1494 A U
1495 A MG 1624 A MG 1635 A MG 1649 A MG 1650 A MG
1653 A C 5 X U 6 X U 32 Y U 33 Y G 34 Y A 38 Y U
1 Z U 2 Z U 4 Z

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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