Interaction between DNA ligase I (1x9n_A) and template DNA/dideoxy terminated DNA/5'-phosphorylated DNA (1x9n_D_B_C)

PDB and SCOP data

PDB ID: 1x9n (all binary interactions in this PDB entry)

Title: Crystal Structure of Human DNA Ligase I bound to 5'-adenylated, nicked DNA

Release date: 2004-11-30

Resolution: 3.0 Å

  • Chain A: 1x9n_A

    Title: DNA ligase I

    Source organism: Homo sapiens

    Number of residues: 688 (56 missing in structure)

  • Chain B: 1x9n_D_B_C

    Title: template DNA/dideoxy terminated DNA/5'-phosphorylated DNA

    Number of residues: 56

    Note: Residues of nucleic acid domain are renumbered to avoid repeating the same residue numbers from different PDB chains.

Buried interface area: 2205.60 Å2

Number of inter-residue contacts at the interface: 174

Number of H-bonds: 31

  • Pairwise interaction

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  • Biological assembly

    Homomer, 1 protein, 3 domains, 1 nucleic acid.

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Create a structural model for this interaction

  • Interface residues in 1x9n_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 303 72 S 38.7 37.9 %
    2 304 73 A 28.3 51.9 %
    3 305 74 R 102.0 70.3 %
    4 306 75 L 43.7 33.1 %
    5 346 115 E 56.9 50.2 %
    6 347 116 L 8.0 23.9 %
    7 348 117 G 27.2 48.6 %
    8 349 118 V 14.3 73.0 %
    9 350 119 G 21.5 76.3 %
    10 351 120 D 16.3 24.9 %
    11 352 121 G 8.5 51.2 %
    12 353 122 V 1.4 6.1 %
    13 415 184 T 14.2 13.2 %
    14 416 185 G 29.2 55.9 %
    15 417 186 S 15.0 13.2 %
    16 418 187 A 20.2 25.1 %
    17 419 188 S 13.7 92.8 %
    18 420 189 T 39.3 61.3 %
    19 423 192 K 1.9 14.5 %
    20 449 218 R 33.1 33.9 %
    21 450 219 L <0.1 0.5 %
    22 451 220 R 41.9 31.8 %
    23 452 221 L 6.7 56.1 %
    24 453 222 G 33.7 64.1 %
    25 454 223 L 13.8 78.5 %
    26 455 224 A 39.4 56.8 %
    27 456 225 E 4.2 7.9 %
    28 457 226 Q 51.8 51.0 %
    29 458 227 S 16.3 80.7 %
    30 493 262 K 27.3 37.2 %
    31 497 266 E 13.5 12.6 %
    32 504 273 K 11.0 24.9 %
    33 546 315 H 9.5 15.1 %
    34 547 316 P 2.7 4.7 %
    35 557 326 R 33.5 28.4 %
    36 568 337 K 5.8 63.9 %
    37 570 339 D 3.8 14.3 %
    38 571 340 G 10.7 89.8 %
    39 572 341 Q 36.2 91.9 %
    40 573 342 R 13.1 74.9 %
    41 588 357 S 16.9 80.7 %
    42 589 358 R 40.4 39.4 %
    43 590 359 N 27.3 32.6 %
    44 592 361 E 43.6 60.2 %
    45 594 363 N 14.9 53.5 %
    46 597 366 K 4.1 10.8 %
    47 621 390 E 2.4 62.4 %
    48 635 404 F 38.6 60.0 %
    49 636 405 Q 33.8 39.1 %
    50 639 408 T 39.8 54.0 %
    51 640 409 T 31.6 35.4 %
    52 641 410 R 11.0 41.5 %
    53 642 411 K 42.4 26.2 %
    54 643 412 R 28.7 39.7 %
    55 644 413 K 24.8 28.1 %
    56 645 414 E <0.1 0.1 %
    57 720 489 E 13.5 31.4 %
    58 737 506 K 3.7 2.9 %
    59 738 507 R 20.1 16.9 %
    60 739 508 S 2.1 6.6 %
    61 740 509 H 7.1 7.9 %
    62 744 513 K 12.2 66.1 %
    63 746 515 K 26.2 41.1 %
    64 765 534 Y 3.3 12.2 %
    65 766 535 L 3.1 5.3 %
    66 767 536 G 4.2 88.7 %
    67 768 537 R 31.0 29.8 %
    68 769 538 G 8.2 58.7 %
    69 770 539 K 75.6 49.9 %
    70 771 540 R 41.8 63.3 %
    71 776 545 G 16.7 93.3 %
    72 777 546 G 7.1 82.7 %
    73 778 547 F 0.2 22.0 %
    74 794 563 C 8.2 100.0 %
    75 795 564 K 64.2 68.7 %
    76 796 565 L 5.9 99.2 %
    77 797 566 G 32.5 96.6 %
    78 798 567 T 54.6 89.6 %
    79 799 568 G 30.9 78.5 %
    80 800 569 F 13.2 87.1 %
    81 801 570 S 26.0 51.1 %
    82 802 571 D 41.4 34.9 %
    83 803 572 E 1.9 1.3 %
    84 850 619 S 22.0 65.6 %
    85 851 620 L 7.3 32.1 %
    86 852 621 S 16.5 98.4 %
    87 853 622 P 34.4 31.5 %
    88 854 623 I 3.3 4.9 %
    89 855 624 Y 26.1 68.5 %
    90 866 635 K 4.1 4.6 %
    91 869 638 S 20.3 100.0 %
    92 870 639 L 12.3 100.0 %
    93 871 640 R 23.7 47.2 %
    94 872 641 F 90.4 92.2 %
    95 873 642 P 29.2 87.7 %
    96 874 643 R 52.3 71.9 %

  • Interface residues in 1x9n_D_B_C

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 8 8:D1 A 8.5 4.9 %
    2 9 9:D1 G 38.4 23.9 %
    3 10 10:D1 T 44.8 28.0 %
    4 11 11:D1 C 87.5 46.4 %
    5 12 12:D1 C 97.7 63.7 %
    6 13 13:D1 G 89.4 48.6 %
    7 14 14:D1 A 139.6 86.7 %
    8 15 15:D1 C 99.4 58.2 %
    9 16 16:D1 G 112.8 61.7 %
    10 17 17:D1 A 93.4 67.0 %
    11 18 18:D1 C 89.7 58.7 %
    12 19 19:D1 G 83.2 47.6 %
    13 20 20:D1 C 63.8 41.1 %
    14 21 21:D1 A 69.3 51.9 %
    15 22 22:D1 T 2.5 1.3 %
    16 23 23:D1 C 72.4 41.5 %
    17 24 24:D1 A 61.2 41.7 %
    18 34 8:B1 T 1.1 0.6 %
    19 35 9:B1 G 63.5 38.3 %
    20 36 10:B1 C 67.3 39.2 %
    21 37 11:B1 G 60.9 34.7 %
    22 38 12:B1 T 106.3 63.0 %
    23 39 13:B1 DOC 121.3 85.4 %
    24 40 1:C1 G 63.1 54.9 %
    25 41 2:C1 T 92.1 65.1 %
    26 42 3:C1 C 75.0 43.1 %
    27 43 4:C1 G 55.3 30.4 %
    28 44 5:C1 G 52.5 30.4 %
    29 45 6:C1 A 25.0 14.2 %
    30 46 7:C1 C 58.8 37.9 %
    31 47 8:C1 T 55.1 30.0 %
    32 48 9:C1 G 54.7 18.4 %

No. Residue no. in chain A structure Residue no. in chain A sequence Residue in chain A Residue no. in chain B structure Residue no. of chain B in PDB Residue in chain B Contact area, Å2 Contact type
1 303 72 S 45 6:C1 A 14.9 H-bond
2 303 72 S 46 7:C1 C 23.8
3 304 73 A 46 7:C1 C 12.0
4 304 73 A 47 8:C1 T 16.3
5 305 74 R 9 9:D1 G 3.8
6 305 74 R 10 10:D1 T 13.8 H-bond
7 305 74 R 11 11:D1 C 32.9
8 305 74 R 12 12:D1 C 8.8
9 305 74 R 44 5:C1 G 0.7
10 305 74 R 45 6:C1 A 10.2
11 305 74 R 46 7:C1 C 23.0
12 305 74 R 47 8:C1 T 8.9
13 306 75 L 47 8:C1 T 29.9
14 306 75 L 48 9:C1 G 13.9
15 346 115 E 36 10:B1 C 34.8 H-bond
16 346 115 E 37 11:B1 G 22.0
17 347 116 L 36 10:B1 C 8.0
18 348 117 G 35 9:B1 G 10.7
19 348 117 G 36 10:B1 C 16.5 H-bond
20 349 118 V 35 9:B1 G 6.4
21 349 118 V 36 10:B1 C 7.9
22 350 119 G 35 9:B1 G 21.5
23 351 120 D 35 9:B1 G 16.3
24 352 121 G 34 8:B1 T 1.1
25 352 121 G 35 9:B1 G 7.3
26 353 122 V 35 9:B1 G 1.4
27 415 184 T 23 23:D1 C 14.2
28 416 185 G 23 23:D1 C 28.8
29 416 185 G 24 24:D1 A 0.4
30 417 186 S 23 23:D1 C 9.1
31 417 186 S 24 24:D1 A 5.9
32 418 187 A 23 23:D1 C <0.1
33 418 187 A 24 24:D1 A 20.2 H-bond
34 419 188 S 23 23:D1 C 9.1
35 419 188 S 24 24:D1 A 4.7
36 420 189 T 23 23:D1 C 9.4
37 420 189 T 24 24:D1 A 29.9 H-bond
38 423 192 K 23 23:D1 C 1.9
39 449 218 R 14 14:D1 A 18.9
40 449 218 R 15 15:D1 C 14.3 H-bond
41 450 219 L 13 13:D1 G <0.1
42 451 220 R 13 13:D1 G 17.6
43 451 220 R 14 14:D1 A 24.3 H-bond
44 452 221 L 13 13:D1 G 6.7
45 453 222 G 12 12:D1 C 19.7
46 453 222 G 13 13:D1 G 14.0 H-bond
47 454 223 L 12 12:D1 C 6.6
48 454 223 L 13 13:D1 G 7.2
49 455 224 A 12 12:D1 C 27.6 H-bond
50 455 224 A 13 13:D1 G 11.8
51 456 225 E 12 12:D1 C 4.2
52 457 226 Q 11 11:D1 C 37.5
53 457 226 Q 12 12:D1 C 14.3
54 458 227 S 11 11:D1 C 4.0
55 458 227 S 12 12:D1 C 12.3 H-bond
56 493 262 K 48 9:C1 G 27.3
57 497 266 E 48 9:C1 G 13.5
58 504 273 K 11 11:D1 C 11.0
59 546 315 H 9 9:D1 G 9.5
60 547 316 P 42 3:C1 C 2.7
61 557 326 R 8 8:D1 A 8.5
62 557 326 R 9 9:D1 G 25.1
63 568 337 K 40 1:C1 G 5.8
64 570 339 D 39 13:B1 DOC 3.8
65 571 340 G 39 13:B1 DOC 10.7
66 572 341 Q 38 12:B1 T 24.9
67 572 341 Q 39 13:B1 DOC 11.4
68 573 342 R 39 13:B1 DOC 13.1 H-bond
69 588 357 S 38 12:B1 T 16.9 H-bond
70 589 358 R 38 12:B1 T 0.7
71 589 358 R 39 13:B1 DOC 24.0
72 589 358 R 40 1:C1 G 15.6
73 590 359 N 37 11:B1 G 6.1
74 590 359 N 38 12:B1 T 17.2 H-bond
75 590 359 N 39 13:B1 DOC 4.0
76 592 361 E 37 11:B1 G 30.9
77 592 361 E 38 12:B1 T 12.7
78 594 363 N 38 12:B1 T 14.9 H-bond
79 597 366 K 38 12:B1 T 4.1
80 621 390 E 39 13:B1 DOC 2.3
81 621 390 E 40 1:C1 G <0.1
82 635 404 F 17 17:D1 A 3.0
83 635 404 F 38 12:B1 T 14.8
84 635 404 F 39 13:B1 DOC 20.8
85 636 405 Q 18 18:D1 C 16.3 H-bond
86 636 405 Q 19 19:D1 G 17.5 H-bond
87 639 408 T 19 19:D1 G 31.7 H-bond
88 639 408 T 20 20:D1 C 6.3
89 639 408 T 37 11:B1 G 1.9
90 640 409 T 19 19:D1 G 9.1
91 640 409 T 20 20:D1 C 22.4
92 641 410 R 20 20:D1 C 11.0
93 642 411 K 20 20:D1 C 11.1
94 642 411 K 21 21:D1 A 31.3 H-bond
95 643 412 R 20 20:D1 C 13.1 H-bond
96 643 412 R 21 21:D1 A 15.6
97 644 413 K 21 21:D1 A 22.4 H-bond
98 644 413 K 22 22:D1 T 2.5
99 645 414 E 21 21:D1 A <0.1
100 720 489 E 39 13:B1 DOC 4.3
101 720 489 E 40 1:C1 G 9.2
102 737 506 K 10 10:D1 T 3.7
103 738 507 R 10 10:D1 T 20.1
104 739 508 S 10 10:D1 T <0.1
105 739 508 S 11 11:D1 C 2.1
106 740 509 H 10 10:D1 T 7.1
107 744 513 K 41 2:C1 T 12.2
108 746 515 K 41 2:C1 T 19.3 H-bond
109 746 515 K 42 3:C1 C 6.9
110 765 534 Y 16 16:D1 G 3.3
111 766 535 L 15 15:D1 C 3.1
112 767 536 G 15 15:D1 C 4.2
113 768 537 R 14 14:D1 A 11.1 H-bond
114 768 537 R 15 15:D1 C 19.9
115 769 538 G 14 14:D1 A 8.2
116 770 539 K 12 12:D1 C 4.2
117 770 539 K 13 13:D1 G 30.3 H-bond
118 770 539 K 14 14:D1 A 32.8 H-bond
119 770 539 K 43 4:C1 G 8.3
120 771 540 R 13 13:D1 G 1.8
121 771 540 R 14 14:D1 A 33.5
122 771 540 R 15 15:D1 C 6.5
123 776 545 G 15 15:D1 C 16.7
124 777 546 G 15 15:D1 C 3.8
125 777 546 G 16 16:D1 G 3.3
126 778 547 F 16 16:D1 G 0.2
127 794 563 C 16 16:D1 G <0.1
128 794 563 C 17 17:D1 A 8.2
129 795 564 K 16 16:D1 G 43.1
130 795 564 K 17 17:D1 A 21.1 H-bond
131 796 565 L 16 16:D1 G 5.9
132 797 566 G 14 14:D1 A 1.2
133 797 566 G 15 15:D1 C 22.2
134 797 566 G 16 16:D1 G 9.0
135 798 567 T 14 14:D1 A 9.7
136 798 567 T 15 15:D1 C 8.8
137 798 567 T 40 1:C1 G 1.8
138 798 567 T 41 2:C1 T 12.8
139 798 567 T 42 3:C1 C 21.6
140 799 568 G 42 3:C1 C 14.5
141 799 568 G 43 4:C1 G 16.4
142 800 569 F 43 4:C1 G 13.2
143 801 570 S 43 4:C1 G 13.6
144 801 570 S 44 5:C1 G 12.4
145 802 571 D 43 4:C1 G 3.9
146 802 571 D 44 5:C1 G 37.5 H-bond
147 803 572 E 44 5:C1 G 1.9
148 850 619 S 17 17:D1 A 5.0
149 850 619 S 18 18:D1 C 17.0 H-bond
150 851 620 L 18 18:D1 C 3.6
151 851 620 L 19 19:D1 G 3.8
152 852 621 S 18 18:D1 C 16.5 H-bond
153 853 622 P 18 18:D1 C 17.4
154 853 622 P 19 19:D1 G 17.1
155 854 623 I 18 18:D1 C 3.3
156 855 624 Y 17 17:D1 A 20.7 H-bond
157 855 624 Y 18 18:D1 C 5.4
158 866 635 K 19 19:D1 G 4.1
159 869 638 S 17 17:D1 A 10.1
160 869 638 S 18 18:D1 C 10.1
161 870 639 L 17 17:D1 A 12.3
162 871 640 R 16 16:D1 G 4.0
163 871 640 R 17 17:D1 A 6.6
164 871 640 R 39 13:B1 DOC 13.1
165 872 641 F 16 16:D1 G 21.8
166 872 641 F 17 17:D1 A 0.7
167 872 641 F 39 13:B1 DOC 13.7
168 872 641 F 40 1:C1 G 30.6
169 872 641 F 41 2:C1 T 23.6
170 873 642 P 16 16:D1 G 22.3
171 873 642 P 17 17:D1 A 5.6
172 873 642 P 41 2:C1 T 1.3
173 874 643 R 41 2:C1 T 22.9
174 874 643 R 42 3:C1 C 29.4 H-bond

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
B1x9n_D_B_C100AMP 56.4312.9

  • Query protein: sp|P49916|DNLI3_HUMAN DNA ligase 3 OS=Homo sapiens GN=LIG3 PE=1 SV=2

    Result domain: 1x9n_A; DNA ligase I

    Alignment data:

    Expectation value = 1.03e-47, Score = 185 bits (469),

    Identities = 33% (124/373), Positive = 50% (188/373), Gaps = 9% (35/373).

    Interface alignment data:

    Interface residues in alignment: 67% (64/96).

    Identities = 42% (27/64), Positive = 58% (37/64), Gaps = 6% (4/64).

    Query: 480 PVQPMLAEACKSVEYAMKKCPNGMFS-EIKYDGERVQVHK-NGDHFSYFSRSLKPVLPHK 537

    P++PMLA + + +K+ F+ E KYDG+R Q+H G FSR+ +

    1x9n_A: 308 PLKPMLAHPTRGISEVLKRFEEAAFTCEYKYDGQRAQIHALEGGEVKIFSRNQE----DN 363

    dssp: -----EEEEE--HHHHHHH-----EEEEEEE--EEEEEEE-----EEEE----- E-


    Query: 538 VAHFKDYIPQA----FPGGHSMILDSEVLLIDNKTGKPLPFGTLGVHKK----AAFQDAN 589

    + D I + P S ILD+E + D + + PF L K+ A+

    1x9n_A: 364 TGKYPDIISRIPKIKLPSVTSFILDTEAVAWDREKKQIQPFQVLTTRKRKEVDASEIQVQ 423

    dssp: ----HHHHH--HHHE------EEEEEEEEEE------E--HHHH---------HHH---E


    Query: 590 VCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIPNRIMFSEMKRVTKALDLADMITRV 649

    VCL+ FD IY N SL+ PL RR+ L +N VE +F+ +A+ + +

    1x9n_A: 424 VCLYAFDLIYLNGESLVREPLSRRRQLLRENFVETEGEFVFATSLDTKDIEQIAEFLEQS 483

    dssp: EEEEEEEEEEE--EE-----HHHHHHHHHHHE--E---EEE--EE----HHHHHHHHHHH


    Query: 650 IQEGLEGLVLK--DVKGTYEPGKR--HWLKVKKDYLNEGAMADTADLVVLGAFYGQGSKG 705

    +++ EGL++K DV TYE KR +WLK+KKDYL+ + DT DLVV+GA+ G+G +

    1x9n_A: 484 VKDSCEGLMVKTLDVDATYEIAKRSHNWLKLKKDYLD--GVGDTLDLVVIGAYLGRGKRA 541

    dssp: HH--EEEEEEEE-------------EEEEEEEHHHHH ---EEEEEEEEEEEEE----E


    Query: 706 GMMSIFLMGCYDPGSQKWCTVTKCAGGHDDATLARLQNELDMVKISKDPSKIPSWLKVNK 765

    G FL+ YD S++ + K G D L L + + PS P +++++

    1x9n_A: 542 GRYGGFLLASYDEDSEELQAICKLGTGFSDEELEEHHQSLKALVL---PSPRP-YVRIDG 597

    dssp: --EEEEEEEEEE----EEEEEEEE-----HHHHHHHHHHHHH-EE ----- -EE---


    Query: 766 IYYPDFIVPDPKKAAVWEITGAEFSKSEAHTA--------DGISIRFPRCTRIRDDKDWK 817

    PD + DP +AVWE+ A+ S S + A GIS+RFPR R+R+DK +

    1x9n_A: 598 AVIPDHWL-DP--SAVWEVKCADLSLSPIYPAARGLVDSDKGISLRFPRFIRVREDKQPE 654

    dssp: -----EEE -- --EEEEEE-EEEEE--------------EEEEE--EEEEE-----HH


    Query: 818 SATNLPQLKELYQ 830

    AT Q+ LY+

    1x9n_A: 655 QATTSAQVACLYR 667

    dssp: H--EHHHHHHHHH


    Download alignment FASTA file