Interaction between DNA ligase 4 (6bkg_A) and DNA (6bkg_T_P_D)

PDB and SCOP data

PDB ID: 6bkg (all binary interactions in this PDB entry)

Title: Human LigIV catalytic domain with bound DNA-adenylate intermediate in closed conformation

Release date: 2018-07-18

Resolution: 2.4 Å

  • Chain A: 6bkg_A

    Title: DNA ligase 4

    Source organism: Homo sapiens

    Number of residues: 621 (21 missing in structure)

  • Chain B: 6bkg_T_P_D

    Title: DNA

    Source organism: synthetic construct

    Number of residues: 37

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

Buried interface area: 2243.01 Å2

Number of inter-residue contacts at the interface: 179

Number of H-bonds: 29

  • Pairwise interaction

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    Download PyMOL visualization script

  • Biological assembly

    Homomer, 1 protein, 1 nucleic acid.

    Download PDB coordinates


Create a structural model for this interaction

  • Interface residues in 6bkg_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 30 31 K 2.6 2.4 %
    2 32 33 R 20.5 14.3 %
    3 35 36 K 5.5 31.7 %
    4 74 75 Q 32.1 28.2 %
    5 81 82 A 38.5 65.3 %
    6 82 83 Y 5.3 42.1 %
    7 83 84 G 32.0 65.1 %
    8 84 85 I 11.7 76.3 %
    9 85 86 K 56.9 48.6 %
    10 86 87 E 0.2 0.5 %
    11 87 88 T 44.6 54.9 %
    12 88 89 M 34.9 39.3 %
    13 91 92 K 24.2 22.7 %
    14 159 160 N 0.1 0.2 %
    15 162 163 K 69.7 39.7 %
    16 164 165 K 9.3 14.6 %
    17 192 193 K 5.3 12.2 %
    18 193 194 D 34.3 62.2 %
    19 194 195 L <0.1 0.9 %
    20 195 196 K 19.2 20.7 %
    21 197 198 G 24.2 40.0 %
    22 199 200 S 24.6 41.7 %
    23 200 201 Q 21.8 38.0 %
    24 201 202 Q 44.7 46.8 %
    25 250 251 L 11.4 50.9 %
    26 251 252 A 13.1 95.6 %
    27 253 254 I 7.1 6.7 %
    28 271 272 E 11.8 80.6 %
    29 272 273 T 7.9 12.0 %
    30 273 274 K 41.1 90.0 %
    31 274 275 L 22.7 47.9 %
    32 275 276 D 3.4 17.5 %
    33 276 277 G 12.9 80.0 %
    34 277 278 E 27.6 96.1 %
    35 278 279 R 50.9 94.9 %
    36 279 280 M 0.6 50.3 %
    37 292 293 S 16.5 89.2 %
    38 293 294 R 61.2 56.6 %
    39 294 295 N 28.5 29.9 %
    40 296 297 Y 53.9 49.5 %
    41 298 299 Y 23.5 42.5 %
    42 331 332 E 25.6 93.9 %
    43 345 346 K 50.8 75.9 %
    44 346 347 G 24.4 61.1 %
    45 347 348 T 21.2 27.1 %
    46 348 349 K 25.2 23.1 %
    47 349 350 F 22.0 54.8 %
    48 350 351 D 43.2 75.5 %
    49 352 353 K 28.4 73.5 %
    50 353 354 R 33.6 49.8 %
    51 354 355 M 2.3 2.2 %
    52 367 368 F 30.2 99.2 %
    53 403 404 V 6.6 44.1 %
    54 427 428 E 5.9 17.1 %
    55 430 431 M 30.1 99.8 %
    56 432 433 K 9.8 98.6 %
    57 441 442 D 5.9 10.0 %
    58 443 444 R 30.0 20.8 %
    59 445 446 E 3.7 5.6 %
    60 447 448 W 10.2 95.1 %
    61 449 450 K 35.8 87.3 %
    62 451 452 K 26.5 98.1 %
    63 453 454 E 8.7 41.8 %
    64 454 455 Y 21.0 28.9 %
    65 470 471 Y 0.3 3.1 %
    66 472 473 G 6.1 98.1 %
    67 473 474 K 58.1 55.6 %
    68 474 475 G 11.1 36.0 %
    69 475 476 S 17.5 16.6 %
    70 476 477 R 46.6 64.1 %
    71 481 482 S 10.4 96.9 %
    72 482 483 H 38.6 77.4 %
    73 483 484 F 1.0 36.0 %
    74 504 505 S 6.2 86.5 %
    75 505 506 R 56.7 58.9 %
    76 506 507 V 10.9 85.6 %
    77 507 508 G 24.7 93.3 %
    78 508 509 S 40.5 80.8 %
    79 509 510 G 28.1 88.7 %
    80 510 511 C 13.3 51.9 %
    81 511 512 T 37.6 47.3 %
    82 512 513 M 31.2 30.5 %
    83 513 514 K 1.1 1.1 %
    84 542 543 T 37.9 45.2 %
    85 544 545 K 2.0 2.3 %
    86 560 561 K 5.5 16.6 %
    87 565 566 V 13.6 46.5 %
    88 566 567 P 9.7 13.0 %
    89 567 568 S 13.6 47.0 %
    90 568 569 D 2.1 2.3 %
    91 569 570 M 16.8 20.2 %
    92 570 571 Y 21.8 66.8 %
    93 575 576 T 22.1 100.0 %
    94 576 577 L 11.1 92.9 %
    95 577 578 R 24.3 53.1 %
    96 578 579 F 78.6 90.3 %
    97 579 580 P 28.3 84.3 %
    98 580 581 R 50.8 95.7 %
    99 582 583 E 7.5 11.3 %

  • Interface residues in 6bkg_T_P_D

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 2 2:T1 T 16.4 9.3 %
    2 3 3:T1 C 53.7 30.1 %
    3 4 4:T1 C 49.2 30.9 %
    4 5 5:T1 G 70.7 39.3 %
    5 6 6:T1 A 116.9 73.6 %
    6 7 7:T1 C 108.2 65.6 %
    7 8 8:T1 G 121.4 76.2 %
    8 9 9:T1 A 97.1 64.7 %
    9 10 10:T1 C 94.7 61.3 %
    10 11 11:T1 G 74.1 45.5 %
    11 12 12:T1 C 60.1 33.5 %
    12 13 13:T1 A 4.5 2.7 %
    13 14 14:T1 T 38.4 19.3 %
    14 15 15:T1 C 34.8 21.3 %
    15 16 16:T1 A 5.8 3.3 %
    16 22 4:P1 G 30.5 16.8 %
    17 23 5:P1 A 12.2 7.4 %
    18 24 6:P1 T 69.6 34.9 %
    19 25 7:P1 G 89.7 55.6 %
    20 26 8:P1 C 71.6 45.0 %
    21 27 9:P1 G 105.7 58.5 %
    22 28 10:P1 T 117.6 78.0 %
    23 29 11:P1 C 104.4 79.1 %
    24 30 1:D1 AMP 305.1 98.5 %
    25 31 2:D1 G 67.4 62.3 %
    26 32 3:D1 T 95.1 62.8 %
    27 33 4:D1 C 80.4 51.2 %
    28 34 5:D1 G 47.2 30.5 %
    29 35 6:D1 G 46.6 28.0 %
    30 36 7:D1 A 1.3 0.7 %
    31 37 8:D1 C 52.7 18.7 %

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 30 31 K 37 8:D1 C 2.6
2 32 33 R 37 8:D1 C 20.5
3 35 36 K 37 8:D1 C 5.5
4 74 75 Q 4 4:T1 C 0.4
5 74 75 Q 5 5:T1 G 31.7
6 81 82 A 26 8:P1 C 23.9
7 81 82 A 27 9:P1 G 14.5
8 82 83 Y 26 8:P1 C 5.3
9 83 84 G 25 7:P1 G 19.8
10 83 84 G 26 8:P1 C 12.2 H-bond
11 84 85 I 25 7:P1 G 5.1
12 84 85 I 26 8:P1 C 6.6
13 85 86 K 25 7:P1 G 33.4 H-bond
14 85 86 K 26 8:P1 C 23.5 H-bond
15 86 87 E 25 7:P1 G 0.2
16 87 88 T 24 6:P1 T 30.1
17 87 88 T 25 7:P1 G 14.5
18 88 89 M 24 6:P1 T 18.1
19 88 89 M 25 7:P1 G 16.8 H-bond
20 91 92 K 23 5:P1 A 2.8
21 91 92 K 24 6:P1 T 21.4 H-bond
22 159 160 N 26 8:P1 C 0.1
23 162 163 K 14 14:T1 T 38.4 H-bond
24 162 163 K 15 15:T1 C 31.3
25 164 165 K 15 15:T1 C 3.5
26 164 165 K 16 16:T1 A 5.8
27 192 193 K 27 9:P1 G 5.3
28 193 194 D 5 5:T1 G 25.1
29 193 194 D 6 6:T1 A 9.2
30 194 195 L 5 5:T1 G <0.1
31 195 196 K 5 5:T1 G 10.8
32 195 196 K 6 6:T1 A 8.4 H-bond
33 197 198 G 37 8:D1 C 24.2
34 199 200 S 3 3:T1 C 9.5
35 199 200 S 4 4:T1 C 15.1
36 200 201 Q 4 4:T1 C 21.8 H-bond
37 201 202 Q 3 3:T1 C 32.9 H-bond
38 201 202 Q 4 4:T1 C 11.8
39 250 251 L 30 1:D1 AMP 11.4
40 251 252 A 30 1:D1 AMP 13.1
41 253 254 I 32 3:D1 T 2.2
42 253 254 I 33 4:D1 C 4.9
43 271 272 E 30 1:D1 AMP 11.8 H-bond
44 272 273 T 30 1:D1 AMP 7.9
45 273 274 K 30 1:D1 AMP 34.5 H-bond
46 273 274 K 31 2:D1 G 6.7
47 274 275 L 30 1:D1 AMP 22.7
48 275 276 D 29 11:P1 C 3.4
49 276 277 G 29 11:P1 C 12.9
50 277 278 E 28 10:P1 T 20.1
51 277 278 E 29 11:P1 C 7.4
52 277 278 E 30 1:D1 AMP <0.1
53 278 279 R 28 10:P1 T 3.0
54 278 279 R 29 11:P1 C 13.5 H-bond
55 278 279 R 30 1:D1 AMP 34.5 H-bond
56 279 280 M 28 10:P1 T 0.6
57 292 293 S 27 9:P1 G 1.3
58 292 293 S 28 10:P1 T 15.1 H-bond
59 293 294 R 28 10:P1 T 9.1
60 293 294 R 29 11:P1 C 23.3
61 293 294 R 30 1:D1 AMP 15.7
62 293 294 R 31 2:D1 G 13.1 H-bond
63 294 295 N 28 10:P1 T 26.4 H-bond
64 294 295 N 29 11:P1 C 2.1
65 296 297 Y 27 9:P1 G 45.9
66 296 297 Y 28 10:P1 T 8.0
67 298 299 Y 27 9:P1 G 21.4
68 298 299 Y 28 10:P1 T 2.1
69 331 332 E 29 11:P1 C 0.3
70 331 332 E 30 1:D1 AMP 25.3
71 345 346 K 9 9:T1 A 5.2
72 345 346 K 10 10:T1 C 9.7
73 345 346 K 27 9:P1 G 2.2
74 345 346 K 28 10:P1 T 16.2 H-bond
75 345 346 K 29 11:P1 C 17.5
76 346 347 G 10 10:T1 C 17.8
77 346 347 G 11 11:T1 G 6.6
78 347 348 T 10 10:T1 C 11.8
79 347 348 T 11 11:T1 G 9.4
80 348 349 K 11 11:T1 G 17.4 H-bond
81 348 349 K 12 12:T1 C 7.8
82 349 350 F 11 11:T1 G 16.8
83 349 350 F 12 12:T1 C 5.2
84 350 351 D 11 11:T1 G 23.9
85 350 351 D 12 12:T1 C 15.6
86 350 351 D 27 9:P1 G 3.6
87 352 353 K 27 9:P1 G 11.5
88 352 353 K 28 10:P1 T 16.9
89 353 354 R 12 12:T1 C 29.2
90 353 354 R 13 13:T1 A 4.5
91 354 355 M 12 12:T1 C 2.3
92 367 368 F 30 1:D1 AMP 30.2
93 403 404 V 30 1:D1 AMP 6.6
94 427 428 E 30 1:D1 AMP <0.1
95 427 428 E 31 2:D1 G 5.9
96 430 431 M 30 1:D1 AMP 30.1
97 432 433 K 30 1:D1 AMP 9.8
98 441 442 D 3 3:T1 C 5.9
99 443 444 R 2 2:T1 T 12.7
100 443 444 R 3 3:T1 C 5.5
101 443 444 R 30 1:D1 AMP 11.5
102 443 444 R 32 3:D1 T 0.3
103 445 446 E 2 2:T1 T 3.7
104 447 448 W 30 1:D1 AMP 10.2
105 449 450 K 30 1:D1 AMP 22.8 H-bond
106 449 450 K 32 3:D1 T 13.0
107 451 452 K 30 1:D1 AMP 7.0
108 451 452 K 31 2:D1 G 11.3 H-bond
109 451 452 K 32 3:D1 T 8.3 H-bond
110 453 454 E 32 3:D1 T 8.7
111 454 455 Y 32 3:D1 T 17.1 H-bond
112 454 455 Y 33 4:D1 C 3.9
113 470 471 Y 8 8:T1 G 0.3
114 472 473 G 7 7:T1 C 6.1
115 473 474 K 6 6:T1 A 38.2
116 473 474 K 7 7:T1 C 19.9 H-bond
117 474 475 G 6 6:T1 A 11.1
118 475 476 S 5 5:T1 G 1.1
119 475 476 S 6 6:T1 A 16.4
120 476 477 R 5 5:T1 G 1.9
121 476 477 R 6 6:T1 A 28.5
122 476 477 R 7 7:T1 C 16.3
123 481 482 S 7 7:T1 C 10.4 H-bond
124 482 483 H 7 7:T1 C 24.9
125 482 483 H 8 8:T1 G 13.7
126 483 484 F 8 8:T1 G 1.0
127 504 505 S 8 8:T1 G 1.7
128 504 505 S 9 9:T1 A 4.5
129 505 506 R 8 8:T1 G 40.2 H-bond
130 505 506 R 9 9:T1 A 16.5
131 506 507 V 7 7:T1 C 0.1
132 506 507 V 8 8:T1 G 10.8
133 507 508 G 6 6:T1 A <0.1
134 507 508 G 7 7:T1 C 19.7
135 507 508 G 8 8:T1 G 5.0
136 508 509 S 6 6:T1 A 5.2
137 508 509 S 7 7:T1 C 10.9
138 508 509 S 8 8:T1 G 1.1
139 508 509 S 31 2:D1 G 0.2
140 508 509 S 32 3:D1 T 8.6
141 508 509 S 33 4:D1 C 14.6
142 509 510 G 33 4:D1 C 16.2
143 509 510 G 34 5:D1 G 11.9
144 510 511 C 34 5:D1 G 13.3
145 511 512 T 34 5:D1 G 18.8
146 511 512 T 35 6:D1 G 18.8
147 512 513 M 34 5:D1 G 3.2
148 512 513 M 35 6:D1 G 26.7 H-bond
149 512 513 M 36 7:D1 A 1.3
150 513 514 K 35 6:D1 G 1.1
151 542 543 T 22 4:P1 G 30.5
152 542 543 T 23 5:P1 A 7.4
153 544 545 K 23 5:P1 A 2.0
154 560 561 K 33 4:D1 C 5.5
155 565 566 V 9 9:T1 A 7.1
156 565 566 V 10 10:T1 C 6.5
157 566 567 P 10 10:T1 C 9.7
158 567 568 S 10 10:T1 C 13.6 H-bond
159 568 569 D 10 10:T1 C 2.1
160 569 570 M 10 10:T1 C 16.8
161 570 571 Y 9 9:T1 A 18.1 H-bond
162 570 571 Y 10 10:T1 C 3.7
163 575 576 T 9 9:T1 A 19.1
164 575 576 T 10 10:T1 C 3.0
165 576 577 L 8 8:T1 G <0.1
166 576 577 L 9 9:T1 A 11.0
167 577 578 R 8 8:T1 G 0.2
168 577 578 R 9 9:T1 A 12.3
169 577 578 R 29 11:P1 C 11.8
170 578 579 F 8 8:T1 G 19.9
171 578 579 F 9 9:T1 A 2.4
172 578 579 F 29 11:P1 C 12.1
173 578 579 F 31 2:D1 G 30.3
174 578 579 F 32 3:D1 T 14.0
175 579 580 P 8 8:T1 G 27.3
176 579 580 P 9 9:T1 A 1.0
177 580 581 R 32 3:D1 T 23.0
178 580 581 R 33 4:D1 C 27.8 H-bond
179 582 583 E 33 4:D1 C 7.5

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A6bkg_A703NA 36.817.6

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

    Result domain: 6bkg_A; DNA ligase 4

    Alignment data:

    Expectation value = 4.38e-38, Score = 155 bits (390),

    Identities = 27% (152/572), Positive = 46% (262/572), Gaps = 12% (69/572).

    Interface alignment data:

    Interface residues in alignment: 97% (96/99).

    Identities = 40% (38/96), Positive = 59% (57/96), Gaps = 3% (3/96).

    Query: 300 HGDV----YLTVKLLLPGVIK--TVYNLNDKQIVKLFSRIFNCNPD--DMARDLE----- 346

    H DV Y ++L+LP + + Y + + + KL+ + N D D + L

    6bkg_A: 58 HKDVTDSFYPAMRLILPQLERERMAYGIKETMLAKLYIELLNLPRDGKDALKLLNYRTPT 117

    dssp: ------HHHHHHH-HHH----------HHHHHHHHHHH-------HHHHHHH------


    Query: 347 --QGDVSE--TIRVFFEQSKSFPPAAKSLLTIQEVDEFLLRLSK---LTKEDEQQQALQD 399

    GD + I F + + K LTIQ+V++ L ++ ++D +++L

    6bkg_A: 118 GTHGDAGDFAMIAYFVLKPRCL---QKGSLTIQQVNDLLDSIASNNSAKRKDLIKKSLLQ 174

    dssp: -----HHHHHHHHH---- -----EHHHHHHHHHHHHHHHH---HHHHHHHHHH


    Query: 400 IASRCTANDLKCIIRLIKHDLKMNSGAKHVLDALDPNAYEAFKASRNLQDVVERVLHNAQ 459

    + ++ +A + K +IR+I DLK+ + + +A E + +L+ V R LH+

    6bkg_A: 175 LITQSSALEQKWLIRMIIKDLKLGVSQQTIFSVFHNDAAELHNVTTDLEKVC-RQLHDPS 233

    dssp: HHH---HHHHHHHHHHHH--------HHHHHHHH---HHHHHHHH--HHHHH HH-----


    Query: 460 EVEKEPGQRRALS-VQASLMTPVQPMLAEACKSVEYAMKKCPNGMFS-EIKYDGERVQVH 517

    LS + +L + +PMLA A +E+ K + F E K DGER+Q+H

    6bkg_A: 234 ---------VGLSDISITLFSAFKPMLA-AIADIEHIEKDMKHQSFYIETKLDGERMQMH 283

    dssp: -----------------EE EE--HHHHHHH-----EEEEE----EEEEEE


    Query: 518 KNGDHFSYFSRSLKPVLPHKVAH-----FKDYIPQAFPGGHSM-ILDSEVLLIDNKTGKP 571

    K+GD + YFSR+ A +I AF + ILD E++ + T

    6bkg_A: 284 KDGDVYKYFSRNGYNYTDQFGASPTEGSLTPFIHNAFKADIQICILDGEMMAYNPNTQTF 343

    dssp: EE--EEEEE-----E-HHHH---------HHHH---E-----EEEEEEEEEEEE----EE


    Query: 572 LPFGT-LGVHKKAAFQDANVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIPNRIMF 630

    + GT + + D C VFD + N+ L L +R + L IP RI

    6bkg_A: 344 MQKGTKFDIKRMVEDSDLQTCYCVFDVLMVNNKKLGHETLRKRYEILSSIFTPIPGRIEI 403

    dssp: E----------- --EEEEEEEEEEEE--EE-----HHHHHHHHHHHE--E---EEE


    Query: 631 SEMKRVTKALDLADMITRVIQEGLEGLVLKDVKGTYEPGKR--HWLKVKKDYLNEGAMAD 688

    + + ++ D + I + EG+++K Y+P KR WLK+K +Y++ + D

    6bkg_A: 404 VQKTQAHTKNEVIDALNEAIDKREEGIMVKQPLSIYKPDKRGEGWLKIKPEYVS--GLMD 461

    dssp: ---EEE--HHHHHHHHHHHHH-----EEEE----------EEEEEEEE-HHH-- --E-


    Query: 689 TADLVVLGAFYGQGSKGGMMSIFLMGCYD---PGSQK--WCTVTKCAGGHDDATLARLQN 743

    D++++G ++G+GS+GGMMS FL + PG + + T+++ G T+ L +

    6bkg_A: 462 ELDILIVGGYWGKGSRGGMMSHFLCAVAEKPPPGEKPSVFHTLSRVGSG---CTMKELYD 518

    dssp: -EEEEEEEEEE--HHH---EEEEEEEEE-----------EEEEEEE--- --HHHHHH


    Query: 744 -ELDMVKISK------DPSKIPSWLKVNKIYYPDFIVPDPKKAAVWEITGAEFSKSEAHT 796

    L + K K PS I + ++Y +P + + +I AE S+ +

    6bkg_A: 519 LGLKLAKYWKPFHRKAPPSSILCGTEKPEVYI------EPCNSVIVQIKAAEIVPSDMYK 572

    dssp: HHHH-HHH-EE---------EE-------EE- -HHH--EEEEE--EEEE-----


    Query: 797 ADGISIRFPRCTRIRDDKDWKSATNLPQLKEL 828

    G ++RFPR +IRDDK+W L L++L

    6bkg_A: 573 T-GCTLRFPRIEKIRDDKEWHECMTLDDLEQL 603

    dssp: - -EEEE--EEEEEE----HHH--EHHHHHHH


    Download alignment FASTA file