Interaction between DNA ligase 3 (3qvg_C) and DNA repair protein XRCC1 (3qvg_D)

PDB and SCOP data

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

Title: XRCC1 bound to DNA ligase

Release date: 2011-06-15

Resolution: 2.3 Å

  • Chain A: 3qvg_C

    Title: DNA ligase 3

    Source organism: Homo sapiens

    Number of residues: 89 (12 missing in structure)

    SCOP family: c.15.1.2

  • Chain B: 3qvg_D

    Title: DNA repair protein XRCC1

    Source organism: Mus musculus

    Number of residues: 106 (2 missing in structure)

    SCOP family: c.15.1.1

Buried interface area: 862.62 Å2

Number of inter-residue contacts at the interface: 67

Number of H-bonds: 12

Number of salt bridges: 7

  • Pairwise interaction

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  • Biological assembly

    Heteromer, 2 proteins, 2 domains.

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Create a structural model for this interaction

  • Interface residues in 3qvg_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 846 13 V 9.3 4.7 %
    2 847 14 L 91.0 82.6 %
    3 848 15 L 20.9 26.0 %
    4 849 16 D 14.2 12.8 %
    5 852 19 T <0.1 0.0 %
    6 853 20 G 1.7 3.1 %
    7 866 33 S 5.1 6.6 %
    8 867 34 R 4.0 3.4 %
    9 869 36 R 29.4 27.7 %
    10 870 37 R 110.6 78.3 %
    11 871 38 Y 59.4 71.5 %
    12 873 40 V 51.6 82.5 %
    13 874 41 A 41.8 100.0 %
    14 875 42 F 31.8 99.0 %
    15 876 43 D 57.5 81.4 %
    16 877 44 G 3.9 58.9 %
    17 878 45 D 32.6 40.5 %
    18 910 77 W 21.0 35.2 %
    19 913 80 I 25.1 100.0 %
    20 914 81 R 72.6 43.8 %
    21 915 82 K 90.5 69.8 %
    22 916 83 R 69.4 49.3 %
    23 917 84 R 19.5 12.1 %

  • Interface residues in 3qvg_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 528 3 E 24.2 11.4 %
    2 529 4 P 55.8 49.6 %
    3 530 5 P 9.4 8.7 %
    4 531 6 D 55.2 38.5 %
    5 532 7 L 68.8 48.8 %
    6 533 8 P 15.1 12.6 %
    7 534 9 V 69.3 53.3 %
    8 535 10 P 66.6 69.3 %
    9 536 11 E 4.7 4.5 %
    10 537 12 L 88.6 82.2 %
    11 538 13 P 5.7 11.4 %
    12 539 14 D 13.2 16.7 %
    13 558 33 R 69.9 45.5 %
    14 561 36 I 14.6 20.4 %
    15 562 37 R 108.9 74.8 %
    16 563 38 Y 15.7 36.9 %
    17 565 40 T 55.7 79.9 %
    18 566 41 A 39.6 100.0 %
    19 567 42 F 17.4 92.8 %
    20 568 43 N 32.2 39.9 %
    21 570 45 E 18.2 21.2 %
    22 571 46 L 0.5 0.8 %
    23 614 89 N 7.8 20.1 %
    24 617 92 Q 5.4 6.4 %

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. in chain B sequence Residue in chain B Contact area, Å2 Contact type
1 846 13 V 535 10 P 0.4
2 846 13 V 537 12 L 3.3
3 846 13 V 614 89 N 0.2
4 846 13 V 617 92 Q 5.4
5 847 14 L 537 12 L 13.2
6 847 14 L 562 37 R 27.0
7 847 14 L 563 38 Y 15.7
8 847 14 L 566 41 A 11.7
9 847 14 L 567 42 F 15.7
10 847 14 L 614 89 N 7.6
11 848 15 L 535 10 P 15.3
12 848 15 L 562 37 R 5.6 H-bond
13 849 16 D 562 37 R 14.2 H-bond, Salt bridge
14 852 19 T 558 33 R <0.1
15 853 20 G 558 33 R 1.7
16 866 33 S 568 43 N 2.0
17 866 33 S 570 45 E 3.0
18 867 34 R 534 9 V 4.0
19 869 36 R 565 40 T 13.7
20 869 36 R 570 45 E 15.2
21 869 36 R 571 46 L 0.5
22 870 37 R 537 12 L 23.1
23 870 37 R 538 13 P 5.7 H-bond
24 870 37 R 539 14 D 13.2 H-bond, Salt bridge
25 870 37 R 565 40 T 23.2
26 870 37 R 566 41 A 13.5 H-bond
27 870 37 R 567 42 F 1.7
28 870 37 R 568 43 N 30.2
29 871 38 Y 534 9 V 19.0
30 871 38 Y 535 10 P 9.4
31 871 38 Y 536 11 E 4.7
32 871 38 Y 537 12 L 26.4
33 873 40 V 558 33 R <0.1
34 873 40 V 561 36 I 14.6
35 873 40 V 562 37 R 19.1
36 873 40 V 565 40 T 17.9
37 874 41 A 537 12 L 11.0
38 874 41 A 562 37 R 15.4 H-bond
39 874 41 A 565 40 T 1.0
40 874 41 A 566 41 A 14.4
41 875 42 F 534 9 V 0.7
42 875 42 F 535 10 P 17.8
43 875 42 F 537 12 L 11.6
44 875 42 F 562 37 R 1.8
45 876 43 D 558 33 R 31.7 H-bond, Salt bridge
46 876 43 D 562 37 R 25.8 Salt bridge
47 877 44 G 558 33 R 3.9
48 878 45 D 558 33 R 32.6 H-bond, Salt bridge
49 910 77 W 534 9 V 21.0
50 913 80 I 532 7 L 0.4
51 913 80 I 533 8 P 0.4
52 913 80 I 534 9 V 16.5
53 913 80 I 535 10 P 7.8
54 914 81 R 530 5 P 3.5
55 914 81 R 531 6 D 31.3
56 914 81 R 532 7 L 29.7 H-bond
57 914 81 R 533 8 P <0.1
58 914 81 R 534 9 V 8.2
59 915 82 K 528 3 E 24.2 Salt bridge
60 915 82 K 529 4 P 36.3 H-bond
61 915 82 K 530 5 P 5.9
62 915 82 K 531 6 D 23.9 H-bond, Salt bridge
63 915 82 K 532 7 L <0.1
64 916 83 R 532 7 L 38.7
65 916 83 R 533 8 P 14.8 H-bond
66 916 83 R 535 10 P 15.9
67 917 84 R 529 4 P 19.5

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: 3qvg_C; DNA ligase 3

    Alignment data:

    Expectation value = 2.68e-53, Score = 183 bits (464),

    Identities = 98% (85/87), Positive = 99% (86/87), Gaps = 0% (0/87).

    Interface alignment data:

    Interface residues in alignment: 100% (23/23).

    Identities = 100% (23/23), Positive = 100% (23/23), Gaps = 0% (0/23).

    Query: 922 KAADETLCQTKVLLDIFTGVRLYLPPSTPDFSRLRRYFVAFDGDLVQEFDMTSATHVLGS 981

    +ADETLCQTKVLLDIFTGVRLYLPPSTPDFSRLRRYFVAFDGDLVQEFDMTSATHVLGS

    3qvg_C: 2 NSADETLCQTKVLLDIFTGVRLYLPPSTPDFSRLRRYFVAFDGDLVQEFDMTSATHVLGS 61

    dssp: ---------EEE-------HHHHHHHHHH---EE--HHHHHH--EEE--


    Query: 982 RDKNPAAQQVSPEWIWACIRKRRLVAP 1008

    RDKNPAAQQVSPEWIWACIRKRRLVAP

    3qvg_C: 62 RDKNPAAQQVSPEWIWACIRKRRLVAP 88

    dssp: -------EEE-HHHHHHHHHH------


    Download alignment FASTA file