Interaction between DNA ligase 4 (3w1b_A) and Artemis-derived peptide (3w1b_B)

PDB and SCOP data

PDB ID: 3w1b (all binary interactions in this PDB entry)

Title: Crystal Structure of Human DNA ligase IV-Artemis Complex (Mercury Derivative)

Release date: 2013-04-03

Resolution: 2.4 Å

  • Chain A: 3w1b_A

    Title: DNA ligase 4

    Source organism: Homo sapiens

    Number of residues: 610 (21 missing in structure)

  • Chain B: 3w1b_B

    Title: Artemis-derived peptide

    Number of residues: 11 (1 missing in structure)

Buried interface area: 433.07 Å2

Number of inter-residue contacts at the interface: 33

Number of H-bonds: 2

  • Pairwise interaction

    Download PDB coordinates

    Download PyMOL visualization script

  • Biological assembly

    Heteromer, 1 protein, 1 peptide.

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Create a structural model for this interaction

  • Interface residues in 3w1b_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 8 9 Q 5.3 7.6 %
    2 10 11 V 2.8 100.0 %
    3 13 14 H 32.2 38.3 %
    4 14 15 V 26.1 100.0 %
    5 15 16 P 11.1 17.8 %
    6 18 19 D 39.7 59.8 %
    7 21 22 S 11.5 25.1 %
    8 22 23 T 9.4 60.2 %
    9 25 26 R 22.6 21.1 %
    10 41 42 E 7.5 9.2 %
    11 42 43 F 32.1 98.1 %
    12 45 46 S 55.5 85.2 %
    13 46 47 W 15.1 99.4 %
    14 48 49 K 21.4 30.6 %
    15 49 50 F 76.2 99.9 %
    16 52 53 A 35.8 49.2 %
    17 53 54 L 28.7 67.3 %

  • Interface residues in 3w1b_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 486 2 V 23.5 13.5 %
    2 487 3 P 62.1 63.8 %
    3 488 4 Q 8.4 7.1 %
    4 489 5 W 140.1 92.7 %
    5 492 8 F 79.9 61.6 %
    6 493 9 F 86.4 79.2 %
    7 494 10 K 26.1 15.8 %
    8 495 11 R 6.6 5.6 %

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. in chain B sequence Residue in chain B Contact area, Å2 Contact type
1 8 9 Q 486 2 V 5.3
2 10 11 V 489 5 W 2.8
3 13 14 H 486 2 V 8.4
4 13 14 H 487 3 P 2.4
5 13 14 H 488 4 Q 5.5
6 13 14 H 489 5 W 15.8
7 14 15 V 489 5 W 26.1
8 15 16 P 489 5 W 11.1
9 18 19 D 489 5 W 13.7 H-bond
10 18 19 D 493 9 F 24.6
11 18 19 D 494 10 K 1.4
12 21 22 S 493 9 F 7.9
13 21 22 S 494 10 K 3.6
14 22 23 T 493 9 F 9.4
15 25 26 R 493 9 F 1.5
16 25 26 R 494 10 K 21.1
17 41 42 E 493 9 F 7.5
18 42 43 F 489 5 W 13.3
19 42 43 F 493 9 F 18.8
20 45 46 S 489 5 W 11.6
21 45 46 S 492 8 F 20.7 H-bond
22 45 46 S 493 9 F 16.6
23 45 46 S 495 11 R 6.6
24 46 47 W 489 5 W 15.1
25 48 49 K 492 8 F 21.4
26 49 50 F 487 3 P 19.8
27 49 50 F 488 4 Q 2.9
28 49 50 F 489 5 W 30.5
29 49 50 F 492 8 F 23.0
30 52 53 A 487 3 P 21.0
31 52 53 A 492 8 F 14.8
32 53 54 L 486 2 V 9.8
33 53 54 L 487 3 P 18.9

Analyse interface in VoroContacts server

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

    Result domain: 3w1b_A; DNA ligase 4

    Alignment data:

    Expectation value = 4.02e-38, Score = 155 bits (390),

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

    Interface alignment data:

    Interface residues in alignment: 0% (0/17).

    Identities = 0% (0/0), Positive = 0% (0/0), Gaps = 0% (0/0).

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

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

    3w1b_A: 58 HKDVTDSFYPAMRLILPQLERERMAYGIKETMLAKLYIELLNLPRDGKDALKLLNYRTPT 117

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


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

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

    3w1b_A: 118 GTHGDAGDFAMIAYFVLKPRCL---QKGSLTIQQVNDLLDSIASNNSAKRKDLIKKSLLQ 174

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


    Query: 400 IASRCTANDLKCIIRLIKHDLKMNSGAKHVLDALDPNAYEAFKASRNLQDVVERVLHNAQ 459

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

    3w1b_A: 175 LITQSSALEQKWLIRMIIKDLKLGVSQQTIFSVFHNDAAELHNVTTDLEKVC-RQLHDPS 233

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


    Query: 460 EVEKEPGQRRALS-VQASLMTPVQPMLAEACKSVEYAMKKCPNGMFS-EIKYDGERVQVH 517

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

    3w1b_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

    3w1b_A: 284 KDGDVYKYFSRNGYNYTDQFGASPTEGSLTPFIHNAFKADIQICILDGEMMAYNPNTQTF 343

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


    Query: 572 LPFGT-LGVHKKAAFQDANVCLFVFDCIYFNDVSLMDRPLCERRKFLHDNMVEIPNRIMF 630

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

    3w1b_A: 344 MQKGTKFDIKRMVEDSDLQTCYCVFDVLMVNNKKLGHETLRKRYEILSSIFTPIPGRIEI 403

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


    Query: 631 SEMKRVTKALDLADMITRVIQEGLEGLVLKDVKGTYEPGKR--HWLKVKKDYLNEGAMAD 688

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

    3w1b_A: 404 VQKTQAHTKNEVIDALNEAIDKREEGIMVKQPLSIYKPDKRGEGWLKIKPEYVS--GLMD 461

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


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

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

    3w1b_A: 462 ELDILIVGGYWGKGSRGGMMSHFLCAVAEKPPPGEKPSVFHTLSRVGSG---CTMKELYD 518

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


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

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

    3w1b_A: 519 LGLKLAKYWKPFHRKAPPSSILCGTEKPEVYI------EPCNSVIVQIKAAEIVPSDMYK 572

    dssp: HHHHHHHH-EE---------EE-------EE- -HHH--EEEEE--EEEE-----


    Query: 797 ADGISIRFPRCTRIRDDKDWKSATNLPQLKEL 828

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

    3w1b_A: 573 T-GCTLRFPRIEKIRDDKEWHECMTLDDLEQL 603

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


    Download alignment FASTA file