Interaction between Poly [ADP-ribose] polymerase 1 (4oqa_D) and Poly [ADP-ribose] polymerase 1 (4oqa_F)

PDB and SCOP data

PDB ID: 4oqa (all binary interactions in this PDB entry)

Title: Structure of Human PARP-1 bound to a DNA double strand break in complex with (2Z)-2-(2,4-dihydroxybenzylidene)-3-oxo-2,3-dihydro-1-benzofuran-7-carboxamide

Release date: 2014-07-02

Resolution: 3.6 Å

  • Chain A: 4oqa_D

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 267 (45 missing in structure)

  • Chain B: 4oqa_F

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 505 (49 missing in structure)

Buried interface area: 694.36 Å2

Number of inter-residue contacts at the interface: 52

Number of H-bonds: 7

Number of salt bridges: 1

  • Pairwise interaction

    Download PDB coordinates

    Download PyMOL visualization script

  • Biological assembly

    Heteromer, 2 proteins, 1 nucleic acid.

    Download PDB coordinates


Create a structural model for this interaction

  • Interface residues in 4oqa_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 40 40 Q 39.8 42.4 %
    2 41 41 S 6.8 47.1 %
    3 42 42 P 32.0 25.6 %
    4 43 43 M 53.2 32.2 %
    5 44 44 F 31.8 26.8 %
    6 45 45 D 89.7 79.3 %
    7 314 207 D 30.6 33.8 %
    8 315 208 V 22.3 25.4 %
    9 316 209 T 21.5 34.5 %
    10 317 210 A 60.3 66.4 %
    11 318 211 W 182.9 83.8 %
    12 319 212 T 51.8 89.1 %
    13 320 213 K 23.3 18.9 %
    14 322 215 M 48.4 28.4 %

  • Interface residues in 4oqa_F

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 559 42 L 3.5 17.5 %
    2 560 43 V 6.1 67.9 %
    3 561 44 D 23.4 71.7 %
    4 563 46 V 25.5 24.2 %
    5 566 49 T 19.0 52.5 %
    6 567 50 N 7.1 64.9 %
    7 568 51 S 16.8 51.6 %
    8 589 72 W 28.7 29.6 %
    9 590 73 G 11.3 82.3 %
    10 591 74 R 34.4 74.6 %
    11 595 78 V 3.3 2.2 %
    12 596 79 I 59.7 74.8 %
    13 597 80 G 28.6 63.3 %
    14 598 81 S 27.8 48.1 %
    15 633 116 K 73.3 80.2 %
    16 634 117 Y 4.6 4.7 %
    17 635 118 P 52.5 46.7 %
    18 636 119 K 13.1 12.1 %
    19 639 122 Y 25.0 47.6 %
    20 726 209 D 3.0 2.6 %
    21 727 210 S 32.9 42.9 %
    22 730 213 L 28.6 66.6 %
    23 731 214 D 46.7 68.2 %
    24 734 217 N 30.7 99.1 %
    25 735 218 R 49.0 44.7 %
    26 738 221 T 19.3 82.7 %
    27 739 222 L 3.8 81.9 %
    28 746 229 M 16.6 12.9 %

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 40 40 Q 591 74 R 3.3
2 40 40 Q 596 79 I 19.9
3 40 40 Q 746 229 M 16.6
4 41 41 S 596 79 I 6.8
5 42 42 P 595 78 V 3.3
6 42 42 P 596 79 I 16.9
7 42 42 P 597 80 G 11.8 H-bond
8 43 43 M 589 72 W 13.1 H-bond
9 43 43 M 597 80 G 12.3
10 43 43 M 598 81 S 27.8
11 44 44 F 589 72 W 15.5
12 44 44 F 590 73 G 2.8
13 44 44 F 596 79 I 9.0
14 44 44 F 597 80 G 4.5
15 45 45 D 566 49 T 19.0 H-bond
16 45 45 D 567 50 N 7.1 H-bond
17 45 45 D 568 51 S 16.8 H-bond
18 45 45 D 590 73 G 8.5
19 45 45 D 591 74 R 31.1 H-bond, Salt bridge
20 45 45 D 596 79 I 7.1
21 314 207 D 635 118 P 29.4
22 314 207 D 636 119 K 1.1
23 315 208 V 727 210 S 22.3
24 316 209 T 635 118 P 0.4
25 316 209 T 727 210 S 2.4
26 316 209 T 731 214 D 18.8 H-bond
27 317 210 A 633 116 K 29.7
28 317 210 A 634 117 Y 4.6
29 317 210 A 635 118 P 22.7
30 317 210 A 636 119 K 3.2
31 318 211 W 559 42 L 3.5
32 318 211 W 560 43 V 6.1
33 318 211 W 561 44 D 4.8
34 318 211 W 633 116 K 43.6
35 318 211 W 639 122 Y 25.0
36 318 211 W 731 214 D 12.8
37 318 211 W 734 217 N 14.9
38 318 211 W 735 218 R 49.0
39 318 211 W 738 221 T 19.3
40 318 211 W 739 222 L 3.8
41 319 212 T 561 44 D 4.1
42 319 212 T 727 210 S 6.0
43 319 212 T 730 213 L 10.9
44 319 212 T 731 214 D 15.1
45 319 212 T 734 217 N 15.7
46 320 213 K 561 44 D 14.5
47 320 213 K 563 46 V <0.1
48 320 213 K 636 119 K 8.8
49 322 215 M 563 46 V 25.4
50 322 215 M 726 209 D 3.0
51 322 215 M 727 210 S 2.3
52 322 215 M 730 213 L 17.7

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: 4oqa_D; Poly [ADP-ribose] polymerase 1

    Alignment data:

    Expectation value = 1.38e-4, Score = 48 bits (112),

    Identities = 32% (26/82), Positive = 54% (44/82), Gaps = 4% (3/82).

    Interface alignment data:

    Interface residues in alignment: 43% (6/14).

    Identities = 17% (1/6), Positive = 50% (3/6), Gaps = 0% (0/6).

    Query: 87 EMAEQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEK 146

    E +++ + V+YAK G A CKKC E I K R+ +V +P + G + WYH C ++

    4oqa_D: 3 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 60

    dssp: ---EEEEE------E------E-----EEEEEEEE----- -EEEEEEE--HHH--


    Query: 147 LERARATTKKIEDLTELEGWEE 168

    R +++ +EL W++

    4oqa_D: 61 GHSIRHPDVEVDGFSELR-WDD 81

    dssp: ------HHHHEE------ HHH


    Download alignment FASTA file