Interaction between DNA ligase 3 (3qvg_A) and DNA repair protein XRCC1 (3qvg_B)

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_A

    Title: DNA ligase 3

    Source organism: Homo sapiens

    Number of residues: 89 (7 missing in structure)

    SCOP family: c.15.1.2

  • Chain B: 3qvg_B

    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: 963.75 Å2

Number of inter-residue contacts at the interface: 69

Number of H-bonds: 12

Number of salt bridges: 6

  • Pairwise interaction

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    Download PyMOL visualization script

  • Biological assembly

    Heteromer, 4 proteins, 4 domains.

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Create a structural model for this interaction

  • Interface residues in 3qvg_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 841 8 L 32.1 20.5 %
    2 845 12 K 56.9 33.9 %
    3 846 13 V 1.9 2.1 %
    4 847 14 L 88.7 80.7 %
    5 848 15 L 24.1 36.2 %
    6 849 16 D 15.6 13.7 %
    7 852 19 T 2.1 2.5 %
    8 853 20 G 2.3 3.6 %
    9 866 33 S 0.9 1.3 %
    10 867 34 R 2.6 2.1 %
    11 869 36 R 37.0 36.7 %
    12 870 37 R 112.0 74.3 %
    13 871 38 Y 70.3 94.1 %
    14 873 40 V 52.0 81.2 %
    15 874 41 A 42.1 100.0 %
    16 875 42 F 29.1 96.2 %
    17 876 43 D 56.9 79.3 %
    18 877 44 G 5.1 52.1 %
    19 878 45 D 31.6 39.5 %
    20 881 48 Q 2.0 1.7 %
    21 910 77 W 18.6 31.4 %
    22 913 80 I 23.8 100.0 %
    23 914 81 R 82.6 45.2 %
    24 915 82 K 78.9 61.2 %
    25 916 83 R 67.5 47.3 %
    26 917 84 R 27.2 19.8 %

  • Interface residues in 3qvg_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 528 3 E 7.0 4.7 %
    2 529 4 P 62.6 54.1 %
    3 530 5 P 10.9 9.8 %
    4 531 6 D 54.1 37.2 %
    5 532 7 L 68.1 48.7 %
    6 533 8 P 18.8 15.1 %
    7 534 9 V 74.8 65.4 %
    8 535 10 P 58.0 55.3 %
    9 536 11 E 21.2 12.7 %
    10 537 12 L 96.1 88.0 %
    11 538 13 P 10.9 22.7 %
    12 539 14 D 10.4 12.5 %
    13 558 33 R 72.6 43.1 %
    14 561 36 I 14.5 18.7 %
    15 562 37 R 108.4 73.6 %
    16 563 38 Y 15.1 35.6 %
    17 565 40 T 54.6 77.7 %
    18 566 41 A 39.2 100.0 %
    19 567 42 F 15.0 95.2 %
    20 568 43 N 27.5 36.0 %
    21 570 45 E 25.7 31.0 %
    22 573 48 D 2.0 1.3 %
    23 614 89 N 13.8 32.8 %
    24 615 90 E 31.0 21.8 %
    25 617 92 Q 51.7 63.7 %

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. in chain B sequence Residue in chain B Contact area, Å2 Contact type
1 841 8 L 614 89 N 1.1
2 841 8 L 615 90 E 31.0
3 845 12 K 538 13 P 1.8
4 845 12 K 614 89 N 3.5
5 845 12 K 617 92 Q 51.7
6 846 13 V 614 89 N 1.9
7 847 14 L 537 12 L 13.5
8 847 14 L 538 13 P 3.6
9 847 14 L 562 37 R 24.2
10 847 14 L 563 38 Y 15.1
11 847 14 L 566 41 A 11.8
12 847 14 L 567 42 F 13.2
13 847 14 L 614 89 N 7.3
14 848 15 L 535 10 P 17.8
15 848 15 L 562 37 R 6.3 H-bond
16 849 16 D 562 37 R 15.6 H-bond, Salt bridge
17 852 19 T 558 33 R 2.1
18 853 20 G 558 33 R 2.3
19 866 33 S 568 43 N 0.9
20 866 33 S 570 45 E <0.1
21 867 34 R 536 11 E 2.6
22 869 36 R 565 40 T 11.3
23 869 36 R 570 45 E 25.6 Salt bridge
24 870 37 R 537 12 L 30.2
25 870 37 R 538 13 P 5.5
26 870 37 R 539 14 D 10.4
27 870 37 R 565 40 T 23.6
28 870 37 R 566 41 A 13.9 H-bond
29 870 37 R 567 42 F 1.8
30 870 37 R 568 43 N 26.6
31 871 38 Y 534 9 V 12.3
32 871 38 Y 535 10 P 9.1 H-bond
33 871 38 Y 536 11 E 18.6
34 871 38 Y 537 12 L 30.3 H-bond
35 873 40 V 561 36 I 14.5
36 873 40 V 562 37 R 19.0
37 873 40 V 565 40 T 18.6
38 874 41 A 537 12 L 11.4
39 874 41 A 562 37 R 16.0 H-bond
40 874 41 A 565 40 T 1.1
41 874 41 A 566 41 A 13.5
42 875 42 F 534 9 V 0.8
43 875 42 F 535 10 P 15.6
44 875 42 F 537 12 L 10.7
45 875 42 F 562 37 R 1.9
46 876 43 D 558 33 R 31.4 H-bond, Salt bridge
47 876 43 D 562 37 R 25.4 Salt bridge
48 877 44 G 558 33 R 5.1
49 878 45 D 558 33 R 31.6 H-bond, Salt bridge
50 881 48 Q 573 48 D 2.0
51 910 77 W 534 9 V 18.6
52 913 80 I 533 8 P <0.1
53 913 80 I 534 9 V 18.6
54 913 80 I 535 10 P 5.2
55 914 81 R 530 5 P 1.9
56 914 81 R 531 6 D 30.4
57 914 81 R 532 7 L 25.8 H-bond
58 914 81 R 533 8 P <0.1
59 914 81 R 534 9 V 24.5
60 915 82 K 528 3 E 7.0
61 915 82 K 529 4 P 35.4 H-bond
62 915 82 K 530 5 P 9.0
63 915 82 K 531 6 D 23.7 H-bond, Salt bridge
64 915 82 K 532 7 L 3.8
65 916 83 R 532 7 L 38.5
66 916 83 R 533 8 P 18.7 H-bond
67 916 83 R 534 9 V <0.1
68 916 83 R 535 10 P 10.2
69 917 84 R 529 4 P 27.2

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_A; 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% (26/26).

    Identities = 100% (26/26), Positive = 100% (26/26), Gaps = 0% (0/26).

    Query: 922 KAADETLCQTKVLLDIFTGVRLYLPPSTPDFSRLRRYFVAFDGDLVQEFDMTSATHVLGS 981

    +ADETLCQTKVLLDIFTGVRLYLPPSTPDFSRLRRYFVAFDGDLVQEFDMTSATHVLGS

    3qvg_A: 2 NSADETLCQTKVLLDIFTGVRLYLPPSTPDFSRLRRYFVAFDGDLVQEFDMTSATHVLGS 61

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


    Query: 982 RDKNPAAQQVSPEWIWACIRKRRLVAP 1008

    RDKNPAAQQVSPEWIWACIRKRRLVAP

    3qvg_A: 62 RDKNPAAQQVSPEWIWACIRKRRLVAP 88

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


    Download alignment FASTA file