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PDBsum entry 3df1
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Top Page protein dna_rna ligands metals Protein-protein interface(s) pores links
Pore analysis for: 3df1 calculated with MOLE 2.0 PDB id
3df1
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 3.17 3.35 37.5 -0.73 -0.77 7.3 83 1 0 0 0 0 0 0  U 723 A U 827 A G 829 A G 830 A A 831 A G 832 A G
833 A U 834 A U 835 A G 846 A C 848 A U 850 A G
851 A U 854 A U 870 A
2 2.76 2.76 51.6 -0.89 -0.71 10.6 87 3 1 0 1 0 0 0  A 595 A A 596 A G 597 A U 598 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 G 633 A C 634 A A
635 A U 636 A C 637 A
3 1.77 2.01 77.9 0.47 -0.04 9.6 88 3 1 1 8 2 0 0  G 671 A U 672 A A 673 A G 674 A A 675 A A 676 A U
709 A G 710 A G 711 A A 712 A G 713 A
4 3.30 3.51 105.7 -0.75 -0.74 7.9 91 4 0 1 1 0 0 0  G 654 A A 655 A G 656 A U 657 A C 658 A U 659 A C
660 A G 661 A U 662 A G 664 A A 665 A G 666 A G
667 A G 668 A G 669 A G 670 A G 671 A U 672 A A
673 A G 674 A A 675 A A 676 A U 709 A G 710 A G
711 A A 712 A G 713 A G 714 A A 715 A G 733 A G
734 A C 735 A C 736 A C 737 A C 738 A U 740 A C
744 A G 745 A A 746 A G 748 A C 806 A A 825 A C
826 A U 827 A G 829 A U 850 A G 851 A G 852 A
5 2.22 2.23 113.4 -0.65 -0.73 8.0 87 3 1 0 2 0 0 0  G 122 A U 123 A C 124 A U 125 A G 126 A G 127 A G
128 A U 133 A G 134 A C 135 A U 137 A G 138 A A
139 A U 218 A U 219 A G 220 A C 221 A C 222 A A
223 A U 224 A U 229 A G 230 A U 231 A G 232 A C
233 A U 261 A A 262 A A 263 A A 313 A C 322 A G
324 A A 325 A G 326 A A 327 A C 328 A U 471 A U
605 A G 606 A A 608 A G 628 A MG 2231 A
6 2.74 2.74 120.4 -0.80 -0.67 6.8 75 5 1 3 0 2 2 0  U 5 A A 7 A G 299 A U 565 A G 566 A G 567 A G 568
A C 569 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 G
821 A U 822 A C 823 A G 824 A A 825 A C 826 A U
827 A G 829 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 U 875 A C 876 A G
877 A
7 3.16 3.35 127.9 -1.22 -0.64 12.7 81 8 0 1 2 1 0 0  U 662 A A 663 A G 664 A A 665 A G 666 A G 667 A G
668 A G 669 A G 670 A G 671 A U 672 A A 673 A G
674 A A 675 A A 676 A U 709 A G 710 A G 711 A A
712 A G 713 A G 714 A A 715 A U 723 A G 733 A G
734 A C 735 A C 736 A C 737 A C 738 A U 740 A C
806 A A 831 A G 832 A G 833 A U 834 A U 835 A U
837 A G 838 A C 839 A A 845 A G 846 A G 847 A
8 1.76 3.01 125.7 -0.64 -0.47 13.5 90 4 3 4 7 1 0 0  G 654 A A 655 A G 656 A U 657 A C 658 A U 659 A C
660 A G 661 A U 662 A G 664 A G 669 A G 670 A G
671 A C 737 A C 738 A C 739 A U 740 A C 744 A G
745 A A 746 A G 748 A A 825 A C 826 A U 827 A G
829 A U 850 A G 851 A G 852 A
9 1.82 1.85 135.4 -0.93 -0.64 9.0 74 8 1 1 3 3 1 0  U 5 A G 6 A A 7 A A 26 A G 27 A A 28 A U 296 A G
297 A G 299 A A 502 A C 503 A C 504 A U 508 A A
509 A C 522 A A 523 A G 524 A C 536 A G 537 A A
539 A G 540 A G 544 A G 550 A U 551 A G 601 A A
602 A U 603 A G 604 A U 605 A G 606 A C 612 A G
628 A A 629 A A 630 A C 631 A U 632 A MG 2306 A
10 1.77 1.90 143.4 -0.74 -0.41 12.7 84 7 1 2 8 3 0 0  U 662 A A 663 A G 664 A A 665 A G 666 A G 667 A G
668 A G 669 A G 670 A G 671 A U 672 A G 713 A G
714 A A 715 A U 723 A G 733 A G 734 A C 735 A C
736 A C 737 A C 738 A U 740 A C 806 A A 831 A G
832 A G 833 A U 834 A U 835 A U 837 A G 838 A C
839 A A 845 A G 846 A G 847 A
11 2.23 2.39 145.0 -0.91 -0.46 15.7 79 9 6 1 9 3 2 0  U 14 A G 15 A A 16 A G 527 A C 528 A U 534 A A
535 A A 831 A G 832 A C 856 A C 857 A C 866 A G
867 A G 886 A G 887 A A 915 A U 916 A G 917 A A
918 A A 919 A G 1392 A U 1393 A A 1394 A C 1397 A
C 1403 A C 1404 A U 1490 A G 1491 A C 1510 A G
1529 A G 1530 A A 1531 A MG 2096 A MG 2170 A
12 2.22 2.24 149.8 -0.76 -0.67 9.8 88 8 2 1 4 0 0 0  A 119 A A 120 A U 121 A G 122 A U 133 A G 134 A C
135 A U 137 A G 138 A A 139 A U 218 A U 219 A G
220 A C 221 A C 222 A A 223 A U 224 A C 233 A G
237 A U 252 A A 253 A U 261 A A 262 A A 263 A G
265 A C 267 A U 268 A C 277 A G 278 A A 279 A C
280 A G 281 A A 282 A U 283 A G 319 A A 320 A C
322 A G 324 A A 325 A G 326 A C 328 A U 471 A A
583 A G 584 A U 594 A A 595 A A 596 A G 645 A G
646 A C 647 A MG 2231 A
13 1.83 1.85 151.9 -0.86 -0.57 9.4 76 10 1 2 6 3 2 0  G 6 A A 7 A A 26 A G 27 A A 28 A A 236 A G 237 A
A 238 A U 239 A G 292 A G 293 A U 294 A U 296 A G
297 A G 299 A A 300 A G 302 A U 304 A A 502 A C
503 A C 504 A U 508 A A 509 A C 522 A A 523 A G
524 A C 536 A G 537 A A 539 A G 540 A G 544 A G
550 A U 551 A A 595 A A 596 A C 611 A C 612 A U
632 A G 633 A C 634 A A 635 A MG 2306 A
14 2.30 2.42 154.6 -1.05 -0.60 14.7 84 14 3 1 6 0 0 0  G 581 A C 582 A A 583 A G 584 A U 594 A A 595 A A
596 A G 645 A G 646 A C 647 A G 668 A G 669 A G
670 A G 671 A U 672 A A 673 A G 674 A A 675 A A
676 A U 709 A G 710 A G 711 A A 712 A G 713 A G
714 A A 715 A C 732 A G 733 A U 762 A G 763 A C
764 A G 765 A A 766 A A 767 A C 806 A A 807 A G
809 A C 810 A C 811 A
15 1.83 1.86 170.1 -0.93 -0.60 8.2 72 9 0 4 3 5 3 0  U 5 A G 6 A A 7 A A 26 A G 27 A A 28 A U 296 A G
297 A G 299 A A 502 A C 503 A C 504 A U 508 A A
509 A C 522 A A 523 A G 524 A C 536 A G 537 A A
539 A G 540 A G 544 A G 550 A U 551 A U 565 A G
566 A G 567 A G 568 A C 569 A C 612 A A 630 A U
632 A G 821 A U 822 A C 823 A G 824 A A 825 A C
826 A U 827 A G 829 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 U 875 A C
876 A G 877 A MG 2306 A
16 1.80 1.89 176.0 -0.50 -0.40 13.3 86 12 5 2 12 2 0 0  G 581 A C 582 A A 583 A G 584 A U 594 A A 595 A A
596 A G 645 A G 646 A C 647 A G 668 A G 669 A G
670 A G 671 A U 672 A G 713 A G 714 A A 715 A C
732 A G 733 A U 762 A G 763 A C 764 A G 765 A A
766 A A 767 A C 806 A A 807 A G 809 A C 810 A C
811 A
17 1.92 1.94 193.1 -1.55 -0.65 17.6 81 16 7 4 3 2 0 0  U 828 A G 829 A U 850 A A 860 A G 861 A C 1071 A
G 1072 A U 1075 A U 1076 A G 1077 A U 1078 A G
1079 A A 1081 A A 1082 A U 1083 A G 1104 A A 1105
A G 1106 A A 1111 A C 1112 A C 1113 A C 1114 A U
1115 A U 1116 A A 1117 A C 1119 A G 1127 A C 1128
A C 1149 A A 1150 A A 1151 A G 1153 A G 1154 A A
1155 A G 1156 A A 1251 A A 1252 A A 1280 A C 1281
A C 1282 A A 1285 A MG 2007 A
18 1.67 1.99 193.6 -0.84 -0.67 9.5 85 9 0 3 2 1 2 0  A 676 A U 677 A U 678 A C 679 A G 691 A U 692 A G
693 A A 706 A U 707 A C 708 A U 709 A C 924 A G
925 A G 926 A G 928 A C 931 A G 933 A C 934 A A
935 A G 966 A C 967 A A 968 A C 1063 A U 1065 A A
1111 A C 1112 A C 1113 A C 1114 A U 1115 A U 1116
A A 1117 A U 1118 A C 1119 A G 1127 A C 1128 A C
1149 A A 1150 A A 1151 A G 1153 A G 1154 A A 1155
A G 1156 A U 1183 A G 1184 A G 1185 A G 1186 A G
1187 A A 1188 A A 1251 A A 1252 A A 1280 A C 1281
A C 1282 A A 1285 A C 1344 A C 1383 A C 1384 A G
1385 A G 1386 A C 1400 A A 1503 A A 1534 A MG
2025 A MG 2192 A
19 1.91 2.04 203.2 -1.31 -0.52 15.8 78 17 9 6 8 5 4 0  U 5 A A 7 A G 299 A U 565 A G 566 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 G 861 A C 862 A C 1071 A
G 1072 A U 1075 A U 1076 A G 1077 A U 1078 A G
1079 A A 1081 A A 1082 A U 1083 A MG 2007 A
20 2.85 2.85 204.8 -0.77 -0.67 7.0 77 8 1 3 1 3 2 0  U 5 A A 7 A G 299 A U 565 A G 566 A G 567 A G 568
A C 569 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 A
665 A G 669 A G 670 A G 671 A U 672 A A 673 A G
674 A A 675 A A 676 A U 709 A G 710 A G 711 A A
712 A G 713 A G 714 A A 715 A A 716 A U 717 A G
727 A A 729 A G 731 A C 732 A G 733 A C 806 A G
818 A G 821 A U 822 A C 823 A U 854 A U 855 A U
871 A A 872 A A 873 A G 874 A U 875 A C 876 A G
877 A G 1526 A U 1527 A
21 1.76 1.82 214.3 -0.85 -0.70 9.0 83 10 0 2 5 0 1 0  C 23 A U 24 A C 25 A A 26 A A 243 A U 244 A A 502
A C 503 A C 504 A U 508 A C 522 A A 523 A G 524 A
C 536 A G 537 A A 539 A G 540 A U 551 A U 552 A A
553 A A 554 A U 555 A C 556 A G 557 A G 558 A A
559 A U 561 A U 562 A G 668 A G 669 A G 670 A G
671 A U 672 A A 673 A G 674 A A 675 A A 676 A U
709 A G 710 A G 711 A A 712 A G 713 A G 714 A A
715 A C 732 A G 733 A A 759 A G 760 A G 761 A U
762 A G 763 A C 764 A G 765 A A 766 A A 767 A C
806 A A 807 A C 810 A C 811 A G 812 A C 883 A U
884 A G 885 A C 896 A C 897 A G 903 A U 904 A U
905 A A 906 A A 907 A A 908 A MG 2306 A
22 1.80 1.85 212.1 -0.98 -0.61 10.6 80 8 5 5 6 4 1 0  G 6 A A 7 A A 26 A G 27 A A 28 A U 137 A G 138 A
C 295 A U 296 A G 297 A A 382 A G 449 A G 450 A A
452 A G 453 A G 454 A G 455 A A 456 A G 457 A U
458 A U 471 A U 472 A U 473 A G 474 A C 475 A U
476 A C 477 A A 502 A C 503 A C 504 A U 508 A A
509 A C 522 A A 523 A G 524 A C 536 A G 537 A A
539 A G 540 A G 544 A G 550 A U 551 A C 611 A C
612 A C 613 A G 615 A G 616 A G 617 A C 618 A A
621 A A 622 A C 623 A U 625 A MG 2306 A
23 1.75 1.99 223.9 -0.49 -0.57 8.4 87 8 1 3 10 2 0 0  C 23 A U 24 A C 25 A A 26 A A 243 A U 244 A G 416
A U 427 A A 430 A G 500 A C 501 A A 502 A C 503 A
C 504 A U 508 A C 522 A A 523 A G 524 A C 536 A G
537 A A 539 A G 540 A G 541 A G 542 A U 551 A U
552 A A 553 A A 554 A U 555 A C 556 A G 557 A G
558 A A 559 A U 561 A U 562 A G 668 A G 669 A G
670 A G 671 A U 672 A G 713 A G 714 A A 715 A C
732 A G 733 A A 759 A G 760 A G 761 A U 762 A G
763 A C 764 A G 765 A A 766 A A 767 A C 806 A A
807 A C 810 A C 811 A G 812 A C 883 A U 884 A G
885 A C 896 A C 897 A G 903 A U 904 A U 905 A A
906 A A 907 A A 908 A MG 2306 A
24 2.78 2.78 229.7 -0.81 -0.65 8.2 82 6 5 7 2 3 2 0  U 5 A G 6 A A 7 A U 137 A G 138 A C 295 A U 296 A
G 297 A G 299 A A 382 A G 449 A G 450 A A 452 A G
453 A G 454 A G 455 A A 456 A G 457 A U 458 A U
471 A U 472 A U 473 A G 474 A C 475 A U 476 A C
477 A U 565 A G 566 A G 567 A G 568 A C 569 A C
611 A C 612 A C 613 A G 615 A G 616 A G 617 A C
618 A A 621 A A 622 A C 623 A U 625 A A 630 A U
632 A G 821 A U 822 A C 823 A G 824 A A 825 A C
826 A U 827 A G 829 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 U 875 A C
876 A G 877 A
25 2.22 2.45 230.9 -0.27 -0.65 5.3 81 5 1 0 6 1 0 0  A 50 A C 52 A A 116 A G 117 A U 118 A A 119 A A
120 A U 121 A G 122 A U 133 A G 134 A C 135 A U
137 A G 138 A A 139 A U 218 A U 219 A G 220 A C
221 A C 222 A A 223 A U 224 A C 233 A G 241 A G
242 A U 252 A U 261 A A 262 A A 263 A G 265 A C
267 A U 268 A C 286 A U 287 A G 318 A G 319 A A
320 A C 322 A G 324 A A 325 A G 326 A C 328 A U
471 A U 562 A A 572 A A 573 A A 574 A A 831 A G
832 A C 856 A C 857 A C 866 A G 867 A U 884 A G
885 A G 886 A G 887 A G 888 A A 889 A G 890 A A
907 A A 908 A A 909 A U 916 A G 917 A A 918 A A
919 A G 1392 A U 1393 A A 1394 A G 1423 A U 1424
A U 1425 A G 1426 A C 1479 A C 1510 A G 1529 A G
1530 A A 1531 A MG 2170 A MG 2231 A
26 1.74 2.04 243.4 -1.02 -0.69 11.6 84 12 4 4 2 1 2 0  A 676 A U 677 A U 678 A C 679 A G 691 A U 692 A G
693 A A 706 A U 707 A C 708 A U 709 A G 925 A G
926 A G 928 A A 937 A A 938 A C 940 A G 941 A G
942 A G 966 A U 1235 A A 1236 A C 1237 A A 1238 A
G 1241 A G 1242 A C 1243 A A 1254 A G 1255 A A
1256 A A 1257 A G 1258 A C 1259 A G 1260 A G 1270
A C 1284 A A 1285 A G 1305 A C 1325 A U 1326 A C
1336 A G 1337 A A 1340 A U 1341 A C 1352 A G 1353
A U 1354 A G 1355 A G 1356 A A 1357 A C 1359 A G
1361 A A 1362 A U 1364 A C 1382 A C 1383 A C 1384
A G 1385 A C 1400 A A 1503 A A 1534 A MG 2143 A
MG 2157 A MG 2349 A
27 2.29 2.33 254.0 -0.87 -0.66 11.1 86 14 1 0 5 0 0 0  A 119 A A 120 A U 121 A G 122 A U 133 A G 134 A C
135 A U 137 A G 138 A A 139 A U 218 A U 219 A G
220 A C 221 A C 222 A A 223 A U 224 A C 233 A G
237 A U 252 A A 253 A U 261 A A 262 A A 263 A G
265 A C 267 A U 268 A C 277 A G 278 A A 279 A C
280 A G 281 A A 282 A U 283 A G 319 A A 320 A C
322 A G 324 A A 325 A G 326 A C 328 A U 471 A G
581 A C 582 A A 583 A G 584 A G 668 A G 669 A G
670 A G 671 A U 672 A A 673 A G 674 A A 675 A A
676 A U 709 A G 710 A G 711 A A 712 A G 713 A G
714 A A 715 A C 732 A G 733 A U 762 A G 763 A C
764 A G 765 A A 766 A A 767 A C 806 A A 807 A G
809 A C 810 A C 811 A MG 2231 A
28 1.72 1.94 267.8 -0.55 -0.55 9.2 84 10 2 3 9 4 1 0  A 665 A G 669 A G 670 A G 671 A U 672 A G 713 A G
714 A A 715 A A 716 A U 717 A C 719 A G 721 A G
722 A C 732 A G 733 A C 806 A C 924 A G 925 A G
926 A G 928 A C 931 A G 933 A C 934 A A 935 A G
966 A C 967 A A 968 A C 1063 A U 1065 A A 1111 A
C 1112 A C 1113 A C 1114 A U 1115 A U 1116 A A
1117 A U 1118 A C 1119 A G 1127 A C 1128 A C 1149
A A 1150 A A 1151 A G 1153 A G 1154 A A 1155 A G
1156 A U 1183 A G 1184 A G 1185 A G 1186 A G 1187
A A 1188 A A 1251 A A 1252 A A 1280 A C 1281 A C
1282 A A 1285 A C 1344 A C 1383 A C 1384 A G 1385
A G 1386 A C 1400 A A 1503 A A 1534 A MG 2025 A
MG 2192 A
29 2.01 2.17 266.6 -0.79 -0.58 12.1 80 11 6 1 10 3 2 0  U 14 A G 15 A A 16 A G 527 A C 528 A U 534 A A
535 A G 668 A G 669 A G 670 A G 671 A U 672 A A
673 A G 674 A A 675 A A 676 A U 709 A G 710 A G
711 A A 712 A G 713 A G 714 A A 715 A C 732 A G
733 A A 766 A A 767 A C 770 A G 771 A U 772 A G
773 A A 781 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 G
886 A G 887 A G 888 A G 890 A U 891 A A 900 A A
901 A G 902 A A 915 A U 916 A A 1394 A C 1397 A C
1403 A C 1404 A G 1405 A U 1490 A G 1491 A C 1510
A G 1511 A G 1514 A G 1515 A G 1516 A A 1519 A C
1520 A MG 2014 A MG 2096 A
30 1.79 1.99 317.6 -0.70 -0.59 10.6 84 12 6 4 9 4 1 0  A 665 A G 669 A G 670 A G 671 A U 672 A G 713 A G
714 A A 715 A A 716 A U 717 A C 719 A G 721 A G
722 A C 732 A G 733 A C 806 A G 925 A G 926 A G
928 A A 937 A A 938 A C 940 A G 941 A G 942 A G
966 A U 1235 A A 1236 A C 1237 A A 1238 A G 1241
A G 1242 A C 1243 A A 1254 A G 1255 A A 1256 A A
1257 A G 1258 A C 1259 A G 1260 A G 1270 A C 1284
A A 1285 A G 1305 A C 1325 A U 1326 A C 1336 A G
1337 A A 1340 A U 1341 A C 1352 A G 1353 A U 1354
A G 1355 A G 1356 A A 1357 A C 1359 A G 1361 A A
1362 A U 1364 A C 1382 A C 1383 A C 1384 A G 1385
A C 1400 A A 1503 A A 1534 A MG 2064 A MG 2143 A
MG 2157 A MG 2192 A MG 2349 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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