Interaction between DNA ligase 4 (6bkf_A) and DNA (6bkf_T_P_D)

PDB and SCOP data

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

Title: Lysyl-adenylate form of human LigIV catalytic domain with bound DNA substrate in open conformation

Release date: 2018-07-18

Resolution: 3.2 Å

  • Chain A: 6bkf_A

    Title: DNA ligase 4

    Source organism: Homo sapiens

    Number of residues: 621 (59 missing in structure)

  • Chain B: 6bkf_T_P_D

    Title: DNA

    Source organism: synthetic construct

    Number of residues: 36

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

Buried interface area: 757.82 Å2

Number of inter-residue contacts at the interface: 55

Number of H-bonds: 10

  • Pairwise interaction

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    Download PyMOL visualization script

  • Biological assembly

    Homomer, 1 protein, 1 nucleic acid.

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Create a structural model for this interaction

  • Interface residues in 6bkf_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 81 82 A 35.1 60.4 %
    2 82 83 Y 6.6 50.0 %
    3 83 84 G 29.6 55.5 %
    4 84 85 I 16.1 53.0 %
    5 85 86 K 52.3 49.4 %
    6 87 88 T 34.9 38.9 %
    7 88 89 M 31.8 43.4 %
    8 162 163 K 37.8 32.5 %
    9 192 193 K 10.3 21.0 %
    10 193 194 D 10.7 14.8 %
    11 195 196 K 11.1 15.2 %
    12 197 198 G 5.9 8.8 %
    13 198 199 V 5.9 17.5 %
    14 199 200 S 46.9 77.5 %
    15 200 201 Q <0.1 0.0 %
    16 201 202 Q 19.9 16.4 %
    17 202 203 T 0.7 8.3 %
    18 250 251 L 2.1 10.6 %
    19 251 252 A 1.0 75.7 %
    20 253 254 I 21.0 17.4 %
    21 275 276 D 4.6 7.8 %
    22 276 277 G 12.0 45.2 %
    23 277 278 E 40.0 37.0 %
    24 278 279 R 18.3 96.1 %
    25 279 280 M <0.1 1.4 %
    26 292 293 S 16.6 95.9 %
    27 293 294 R 66.7 66.7 %
    28 294 295 N 30.3 33.0 %
    29 295 296 G <0.1 0.2 %
    30 296 297 Y 55.0 54.6 %
    31 298 299 Y 33.6 42.1 %
    32 331 332 E 7.6 94.9 %
    33 344 345 Q 9.1 8.1 %
    34 443 444 R 33.7 23.8 %
    35 449 450 K 25.1 93.5 %
    36 451 452 K 25.0 30.4 %
    37 454 455 Y 0.3 0.4 %

  • Interface residues in 6bkf_T_P_D

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 4 4:T1 C 48.6 28.2 %
    2 5 5:T1 G 30.7 16.2 %
    3 6 6:T1 A 21.9 12.5 %
    4 11 11:T1 G 9.1 4.9 %
    5 14 14:T1 T 11.2 5.7 %
    6 15 15:T1 C 26.6 16.0 %
    7 24 6:P1 T 33.2 15.8 %
    8 25 7:P1 G 92.3 55.5 %
    9 26 8:P1 C 69.9 44.5 %
    10 27 9:P1 G 90.9 49.3 %
    11 28 10:P1 T 109.4 66.5 %
    12 29 11:P1 C 77.1 55.6 %
    13 30 2:D1 G 71.6 59.9 %
    14 31 3:D1 T 65.0 40.6 %
    15 32 4:D1 C 0.3 0.2 %

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 81 82 A 26 8:P1 C 24.1
2 81 82 A 27 9:P1 G 11.0
3 82 83 Y 26 8:P1 C 6.6
4 83 84 G 25 7:P1 G 17.9
5 83 84 G 26 8:P1 C 11.7 H-bond
6 84 85 I 25 7:P1 G 6.1
7 84 85 I 26 8:P1 C 10.0
8 85 86 K 25 7:P1 G 34.8
9 85 86 K 26 8:P1 C 17.5
10 87 88 T 24 6:P1 T 19.2
11 87 88 T 25 7:P1 G 15.8 H-bond
12 88 89 M 24 6:P1 T 14.0
13 88 89 M 25 7:P1 G 17.8 H-bond
14 162 163 K 14 14:T1 T 11.2
15 162 163 K 15 15:T1 C 26.6
16 192 193 K 27 9:P1 G 10.3
17 193 194 D 6 6:T1 A 10.7
18 195 196 K 6 6:T1 A 11.1
19 197 198 G 5 5:T1 G 5.9
20 198 199 V 5 5:T1 G 5.9
21 199 200 S 4 4:T1 C 28.0 H-bond
22 199 200 S 5 5:T1 G 18.9
23 200 201 Q 5 5:T1 G <0.1
24 201 202 Q 4 4:T1 C 19.9
25 202 203 T 4 4:T1 C 0.7
26 250 251 L 30 2:D1 G 2.1
27 251 252 A 30 2:D1 G 1.0
28 253 254 I 31 3:D1 T 21.0
29 275 276 D 29 11:P1 C 4.6
30 276 277 G 29 11:P1 C 12.0
31 277 278 E 27 9:P1 G 4.8
32 277 278 E 28 10:P1 T 25.3
33 277 278 E 29 11:P1 C 10.0
34 278 279 R 28 10:P1 T 2.4
35 278 279 R 29 11:P1 C 15.9 H-bond
36 279 280 M 28 10:P1 T <0.1
37 292 293 S 28 10:P1 T 16.6 H-bond
38 293 294 R 28 10:P1 T 10.9
39 293 294 R 29 11:P1 C 27.1
40 293 294 R 30 2:D1 G 28.6 H-bond
41 294 295 N 28 10:P1 T 30.3 H-bond
42 295 296 G 28 10:P1 T <0.1
43 296 297 Y 27 9:P1 G 42.0
44 296 297 Y 28 10:P1 T 13.0
45 298 299 Y 27 9:P1 G 22.8 H-bond
46 298 299 Y 28 10:P1 T 10.8
47 331 332 E 29 11:P1 C 7.6
48 344 345 Q 11 11:T1 G 9.1
49 443 444 R 30 2:D1 G 19.9
50 443 444 R 31 3:D1 T 13.8
51 449 450 K 30 2:D1 G 14.3
52 449 450 K 31 3:D1 T 10.8
53 451 452 K 30 2:D1 G 5.7
54 451 452 K 31 3:D1 T 19.3 H-bond
55 454 455 Y 32 4:D1 C 0.3

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A6bkf_A701AMP 292.862.0

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

    Result domain: 6bkf_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: 100% (37/37).

    Identities = 43% (16/37), Positive = 54% (20/37), Gaps = 0% (0/37).

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

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

    6bkf_A: 58 HKDVTDSFYPAMRLILPQLERERMAYGIKETMLAKLYIELLNLPRDGKDALKLLNYRTPT 117

    dssp: ------HHHHHHH-HHH----------HHHHHHHHHHHH------HHHHHHH---


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

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

    6bkf_A: 118 GTHGDAGDFAMIAYFVLKPRCL---QKGSLTIQQVNDLLDSIASNNSAKRKDLIKKSLLQ 174

    dssp: -HHHHHHHHHHHH-- -----EHHHHHHHHHHHHHHHH---HHHHHHHHHH


    Query: 400 IASRCTANDLKCIIRLIKHDLKMNSGAKHVLDALDPNAYEAFKASRNLQDVVERVLHNAQ 459

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

    6bkf_A: 175 LITQSSALEQKWLIRMIIKDLKLGVSQQTIFSVFHNDAAELHNVTTDLEKVC-RQLHDPS 233

    dssp: HHH---HHHHHHHHHHH---------HHHHHHHH---HHHHHH----HHHHH HH-----


    Query: 460 EVEKEPGQRRALS-VQASLMTPVQPMLAEACKSVEYAMKKCPNGMFS-EIKYDGERVQVH 517

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

    6bkf_A: 234 ---------VGLSDISITLFSAFKPMLA-AIADIEHIEKDMKHQSFYIETKLDGERMQMH 283

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


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

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

    6bkf_A: 284 KDGDVYKYFSRNGYNYTDQFGASPTEGSLTPFIHNAFKADIQICILDGEMMAYNPNTQTF 343

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


    Query: 572 LPFGT-LGVHKKAAFQDANVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIPNRIMF 630

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

    6bkf_A: 344 MQKGTKFDIKRMVEDSDLQTCYCVFDVLMVNNKKLGHETLRKRYEILSSIFTPIPGRIEI 403

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


    Query: 631 SEMKRVTKALDLADMITRVIQEGLEGLVLKDVKGTYEPGKR--HWLKVKKDYLNEGAMAD 688

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

    6bkf_A: 404 VQKTQAHTKNEVIDALNEAIDKREEGIMVKQPLSIYKPDKRGEGWLKIKPEYVS--GLMD 461

    dssp: --EEEE--HHHHHHHHHHHHH-----EEEE--------------EEEE------ -HHH


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

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

    6bkf_A: 462 ELDILIVGGYWGKGSRGGMMSHFLCAVAEKPPPGEKPSVFHTLSRVGSG---CTMKELYD 518

    dssp: -EEEEEEEEEE-- ----EEEEEEEEE---- ----EEEEEEEE-- ---HHHHH


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

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

    6bkf_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

    6bkf_A: 573 T-GCTLRFPRIEKIRDDKEWHECMTLDDLEQL 603

    dssp: - -EEEE--EEEEE-----HHH--EHHHHHHH


    Download alignment FASTA file