Interaction between Poly [ADP-ribose] polymerase 1 (4oqa_A) and Poly [ADP-ribose] polymerase 1 (4oqa_C)

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_A

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 267 (45 missing in structure)

  • Chain B: 4oqa_C

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 505 (49 missing in structure)

Buried interface area: 703.67 Å2

Number of inter-residue contacts at the interface: 54

Number of H-bonds: 6

Number of salt bridges: 1

  • Pairwise interaction

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    Download PyMOL visualization script

  • Biological assembly

    Heteromer, 2 proteins, 1 nucleic acid.

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Create a structural model for this interaction

  • Interface residues in 4oqa_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 40 40 Q 42.8 45.6 %
    2 41 41 S 7.3 49.0 %
    3 42 42 P 32.9 26.4 %
    4 43 43 M 51.9 31.3 %
    5 44 44 F 32.3 27.2 %
    6 45 45 D 89.6 80.2 %
    7 46 46 G 0.2 1.0 %
    8 314 207 D 33.4 37.0 %
    9 315 208 V 20.7 23.5 %
    10 316 209 T 21.2 33.7 %
    11 317 210 A 61.7 70.0 %
    12 318 211 W 184.3 84.1 %
    13 319 212 T 51.8 88.4 %
    14 320 213 K 25.9 21.1 %
    15 322 215 M 47.9 27.9 %

  • Interface residues in 4oqa_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 559 42 L 3.6 18.3 %
    2 560 43 V 6.3 69.7 %
    3 561 44 D 23.7 73.1 %
    4 563 46 V 24.1 22.8 %
    5 564 47 K 0.6 0.4 %
    6 566 49 T 18.8 51.7 %
    7 567 50 N 7.5 66.2 %
    8 568 51 S 17.7 53.6 %
    9 589 72 W 27.8 28.9 %
    10 590 73 G 11.7 83.9 %
    11 591 74 R 34.9 74.8 %
    12 595 78 V 3.7 2.5 %
    13 596 79 I 60.7 76.6 %
    14 597 80 G 28.6 63.0 %
    15 598 81 S 27.2 46.6 %
    16 633 116 K 74.4 81.2 %
    17 634 117 Y 5.7 5.7 %
    18 635 118 P 54.8 49.6 %
    19 636 119 K 17.0 15.6 %
    20 639 122 Y 25.4 47.3 %
    21 726 209 D 3.7 3.2 %
    22 727 210 S 32.8 42.1 %
    23 730 213 L 28.2 65.8 %
    24 731 214 D 45.7 66.3 %
    25 734 217 N 30.7 99.2 %
    26 735 218 R 47.5 43.6 %
    27 738 221 T 19.3 83.0 %
    28 739 222 L 3.4 77.9 %
    29 746 229 M 18.4 14.4 %

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 40 40 Q 591 74 R 4.5
2 40 40 Q 596 79 I 19.9
3 40 40 Q 746 229 M 18.4
4 41 41 S 596 79 I 7.3
5 42 42 P 595 78 V 3.7
6 42 42 P 596 79 I 17.8
7 42 42 P 597 80 G 11.3 H-bond
8 43 43 M 589 72 W 11.9 H-bond
9 43 43 M 597 80 G 12.7
10 43 43 M 598 81 S 27.2
11 44 44 F 589 72 W 15.8
12 44 44 F 590 73 G 2.7
13 44 44 F 596 79 I 9.2
14 44 44 F 597 80 G 4.5
15 45 45 D 566 49 T 18.6 H-bond
16 45 45 D 567 50 N 7.5 H-bond
17 45 45 D 568 51 S 17.7 H-bond
18 45 45 D 589 72 W <0.1
19 45 45 D 590 73 G 8.9
20 45 45 D 591 74 R 30.4 H-bond, Salt bridge
21 45 45 D 596 79 I 6.5
22 46 46 G 566 49 T 0.2
23 314 207 D 635 118 P 30.9
24 314 207 D 636 119 K 2.5
25 315 208 V 727 210 S 20.7
26 316 209 T 635 118 P 1.3
27 316 209 T 727 210 S 2.6
28 316 209 T 731 214 D 17.3
29 317 210 A 633 116 K 29.6
30 317 210 A 634 117 Y 5.7
31 317 210 A 635 118 P 22.7
32 317 210 A 636 119 K 3.7
33 318 211 W 559 42 L 3.6
34 318 211 W 560 43 V 6.3
35 318 211 W 561 44 D 5.1
36 318 211 W 633 116 K 44.8
37 318 211 W 639 122 Y 25.4
38 318 211 W 731 214 D 13.3
39 318 211 W 734 217 N 15.6
40 318 211 W 735 218 R 47.5
41 318 211 W 738 221 T 19.3
42 318 211 W 739 222 L 3.4
43 319 212 T 561 44 D 4.0
44 319 212 T 727 210 S 6.6
45 319 212 T 730 213 L 10.9
46 319 212 T 731 214 D 15.2
47 319 212 T 734 217 N 15.1
48 320 213 K 561 44 D 14.6
49 320 213 K 564 47 K 0.6
50 320 213 K 636 119 K 10.7
51 322 215 M 563 46 V 24.1
52 322 215 M 726 209 D 3.7
53 322 215 M 727 210 S 2.9
54 322 215 M 730 213 L 17.3

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_A; 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: 47% (7/15).

    Identities = 29% (2/7), Positive = 57% (4/7), Gaps = 0% (0/7).

    Query: 87 EMAEQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEK 146

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

    4oqa_A: 3 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 60

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


    Query: 147 LERARATTKKIEDLTELEGWEE 168

    R +++ +EL W++

    4oqa_A: 61 GHSIRHPDVEVDGFSELR-WDD 81

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


    Download alignment FASTA file