Interaction between DNA ligase 3 (3pc8_D) and DNA repair protein XRCC1 (3pc8_B)

PDB and SCOP data

PDB ID: 3pc8 (all binary interactions in this PDB entry)

Title: X-ray crystal structure of the heterodimeric complex of XRCC1 and DNA ligase III-alpha BRCT domains.

Release date: 2011-06-15

Resolution: 2.3 Å

  • Chain A: 3pc8_D

    Title: DNA ligase 3

    Source organism: Homo sapiens

    Number of residues: 88 (10 missing in structure)

    SCOP family: c.15.1.2

  • Chain B: 3pc8_B

    Title: DNA repair protein XRCC1

    Source organism: Mus musculus

    Number of residues: 98 (2 missing in structure)

    SCOP family: c.15.1.1

Buried interface area: 590.81 Å2

Number of inter-residue contacts at the interface: 48

Number of H-bonds: 5

Number of salt bridges: 2

  • 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 3pc8_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 845 11 K 3.2 1.7 %
    2 846 12 V 56.2 45.5 %
    3 847 13 L 87.8 93.1 %
    4 848 14 L 4.7 8.4 %
    5 849 15 D 14.1 16.8 %
    6 867 33 R 15.2 13.9 %
    7 869 35 R 46.3 42.6 %
    8 870 36 R 106.1 77.4 %
    9 871 37 Y 55.1 89.0 %
    10 873 39 V 51.0 82.8 %
    11 874 40 A 43.6 100.0 %
    12 875 41 F 21.8 68.0 %
    13 876 42 D 22.8 84.1 %
    14 878 44 D 13.1 27.0 %
    15 910 76 W 2.9 5.9 %
    16 913 79 I 18.6 92.0 %
    17 914 80 R 14.7 8.6 %
    18 916 82 R 13.7 9.1 %

  • Interface residues in 3pc8_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 535 2 P 81.9 44.4 %
    2 536 3 E 10.0 9.4 %
    3 537 4 L 101.5 85.5 %
    4 538 5 P 19.3 34.0 %
    5 539 6 D 9.2 12.0 %
    6 558 25 R 13.1 17.8 %
    7 561 28 I 16.4 21.7 %
    8 562 29 R 107.7 80.7 %
    9 563 30 Y 17.0 43.5 %
    10 565 32 T 67.0 95.3 %
    11 566 33 A 39.2 100.0 %
    12 567 34 F 18.5 100.0 %
    13 568 35 N 29.2 43.8 %
    14 569 36 G 4.5 41.3 %
    15 570 37 E 0.4 0.5 %
    16 571 38 L 13.0 20.9 %
    17 614 81 N 14.1 30.7 %
    18 617 84 Q 28.8 33.4 %

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
1 845 11 K 562 29 R 3.2
2 846 12 V 537 4 L 9.8
3 846 12 V 538 5 P 13.9
4 846 12 V 567 34 F 3.5
5 846 12 V 614 81 N 0.6
6 846 12 V 617 84 Q 28.4
7 847 13 L 537 4 L 8.7
8 847 13 L 562 29 R 23.0
9 847 13 L 563 30 Y 17.0
10 847 13 L 566 33 A 11.4
11 847 13 L 567 34 F 13.8
12 847 13 L 614 81 N 13.5
13 847 13 L 617 84 Q 0.4
14 848 14 L 562 29 R 4.7
15 849 15 D 562 29 R 14.1 H-bond, Salt bridge
16 867 33 R 535 2 P 13.1
17 867 33 R 536 3 E 2.2
18 869 35 R 561 28 I 4.2
19 869 35 R 565 32 T 24.1
20 869 35 R 569 36 G 4.5
21 869 35 R 570 37 E 0.4
22 869 35 R 571 38 L 13.0
23 870 36 R 537 4 L 22.6
24 870 36 R 538 5 P 5.4 H-bond
25 870 36 R 539 6 D 9.2
26 870 36 R 565 32 T 25.3
27 870 36 R 566 33 A 13.2 H-bond
28 870 36 R 567 34 F 1.2
29 870 36 R 568 35 N 29.2
30 871 37 Y 535 2 P 15.1
31 871 37 Y 536 3 E 7.8
32 871 37 Y 537 4 L 32.2 H-bond
33 873 39 V 561 28 I 12.2
34 873 39 V 562 29 R 21.8
35 873 39 V 565 32 T 17.0
36 874 40 A 537 4 L 12.3
37 874 40 A 562 29 R 16.2 H-bond
38 874 40 A 565 32 T 0.5
39 874 40 A 566 33 A 14.6
40 875 41 F 535 2 P 3.9
41 875 41 F 537 4 L 15.9
42 875 41 F 562 29 R 2.0
43 876 42 D 562 29 R 22.8 Salt bridge
44 878 44 D 558 25 R 13.1
45 910 76 W 535 2 P 2.9
46 913 79 I 535 2 P 18.6
47 914 80 R 535 2 P 14.7
48 916 82 R 535 2 P 13.7

Analyse interface in VoroContacts server
Chain Protein Residue no. Ligand name Contact area with same domain Contact area with other domain
A3pc8_D2TRS 69.069.5

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

    Result domain: 3pc8_D; DNA ligase 3

    Alignment data:

    Expectation value = 4.10e-52, Score = 180 bits (455),

    Identities = 98% (84/86), Positive = 99% (85/86), Gaps = 0% (0/86).

    Interface alignment data:

    Interface residues in alignment: 100% (18/18).

    Identities = 100% (18/18), Positive = 100% (18/18), Gaps = 0% (0/18).

    Query: 923 AADETLCQTKVLLDIFTGVRLYLPPSTPDFSRLRRYFVAFDGDLVQEFDMTSATHVLGSR 982

    +ADETL QTKVLLDIFTGVRLYLPPSTPDFSRLRRYFVAFDGDLVQEFDMTSATHVLGSR

    3pc8_D: 2 SADETLSQTKVLLDIFTGVRLYLPPSTPDFSRLRRYFVAFDGDLVQEFDMTSATHVLGSR 61

    dssp: ----------EEE-------HHHHHHHHHH---EE-----HHH--EEE---


    Query: 983 DKNPAAQQVSPEWIWACIRKRRLVAP 1008

    DKNPAAQQVSPEWIWACIRKRRLVAP

    3pc8_D: 62 DKNPAAQQVSPEWIWACIRKRRLVAP 87

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


    Download alignment FASTA file