Interaction between Poly [ADP-ribose] polymerase 1 (4oqb_A) and Poly [ADP-ribose] polymerase 1 (4oqb_C)

PDB and SCOP data

PDB ID: 4oqb (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-{4-[2-(morpholin-4-yl)ethoxy]benzylidene}-3-oxo-2,3-dihydro-1-benzofuran-7-carboxamide

Release date: 2014-07-02

Resolution: 3.4 Å

  • Chain A: 4oqb_A

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 267 (45 missing in structure)

  • Chain B: 4oqb_C

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 505 (49 missing in structure)

Buried interface area: 713.73 Å2

Number of inter-residue contacts at the interface: 55

Number of H-bonds: 5

Number of salt bridges: 1

  • Pairwise interaction

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  • Biological assembly

    Heteromer, 2 proteins, 1 nucleic acid.

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Create a structural model for this interaction

  • Interface residues in 4oqb_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 40 40 Q 44.6 47.9 %
    2 41 41 S 7.4 49.4 %
    3 42 42 P 33.6 27.1 %
    4 43 43 M 53.9 32.4 %
    5 44 44 F 32.1 26.8 %
    6 45 45 D 89.7 81.2 %
    7 46 46 G 0.7 3.9 %
    8 314 207 D 33.2 37.2 %
    9 315 208 V 21.9 24.9 %
    10 316 209 T 20.6 32.9 %
    11 317 210 A 60.6 68.0 %
    12 318 211 W 183.1 84.1 %
    13 319 212 T 51.5 89.4 %
    14 320 213 K 26.8 22.0 %
    15 322 215 M 53.9 31.6 %

  • Interface residues in 4oqb_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 559 42 L 3.1 16.3 %
    2 560 43 V 6.4 70.4 %
    3 561 44 D 24.0 74.1 %
    4 563 46 V 23.8 22.5 %
    5 564 47 K 0.9 0.6 %
    6 566 49 T 18.9 52.2 %
    7 567 50 N 7.6 68.0 %
    8 568 51 S 17.9 54.9 %
    9 589 72 W 30.3 31.5 %
    10 590 73 G 12.4 86.1 %
    11 591 74 R 34.8 75.1 %
    12 595 78 V 3.3 2.2 %
    13 596 79 I 61.0 76.3 %
    14 597 80 G 28.8 63.1 %
    15 598 81 S 28.5 49.2 %
    16 633 116 K 73.7 81.1 %
    17 634 117 Y 5.2 5.3 %
    18 635 118 P 53.4 47.8 %
    19 636 119 K 15.0 13.9 %
    20 639 122 Y 25.8 47.2 %
    21 726 209 D 6.4 5.5 %
    22 727 210 S 36.5 47.3 %
    23 730 213 L 29.7 70.0 %
    24 731 214 D 45.4 67.6 %
    25 734 217 N 30.3 99.5 %
    26 735 218 R 49.2 44.8 %
    27 738 221 T 19.3 82.7 %
    28 739 222 L 3.7 79.7 %
    29 746 229 M 18.6 14.7 %

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 40 40 Q 591 74 R 4.8
2 40 40 Q 596 79 I 21.2
3 40 40 Q 746 229 M 18.6
4 41 41 S 596 79 I 7.4
5 42 42 P 595 78 V 3.3
6 42 42 P 596 79 I 17.8
7 42 42 P 597 80 G 12.5 H-bond
8 43 43 M 589 72 W 13.5 H-bond
9 43 43 M 597 80 G 11.9
10 43 43 M 598 81 S 28.5
11 44 44 F 589 72 W 16.7
12 44 44 F 590 73 G 2.8
13 44 44 F 596 79 I 8.2
14 44 44 F 597 80 G 4.4
15 45 45 D 566 49 T 18.2
16 45 45 D 567 50 N 7.6 H-bond
17 45 45 D 568 51 S 17.9 H-bond
18 45 45 D 589 72 W <0.1
19 45 45 D 590 73 G 9.6
20 45 45 D 591 74 R 30.0 H-bond, Salt bridge
21 45 45 D 596 79 I 6.4
22 46 46 G 566 49 T 0.7
23 314 207 D 635 118 P 31.5
24 314 207 D 636 119 K 1.7
25 315 208 V 727 210 S 21.9
26 316 209 T 635 118 P 0.4
27 316 209 T 727 210 S 2.7
28 316 209 T 731 214 D 17.5
29 317 210 A 633 116 K 30.8
30 317 210 A 634 117 Y 5.2
31 317 210 A 635 118 P 21.4
32 317 210 A 636 119 K 3.2
33 318 211 W 559 42 L 3.1
34 318 211 W 560 43 V 6.4
35 318 211 W 561 44 D 4.3
36 318 211 W 633 116 K 42.8
37 318 211 W 639 122 Y 25.8
38 318 211 W 731 214 D 12.9
39 318 211 W 734 217 N 15.5
40 318 211 W 735 218 R 49.2
41 318 211 W 738 221 T 19.3
42 318 211 W 739 222 L 3.7
43 319 212 T 561 44 D 4.1
44 319 212 T 727 210 S 6.6
45 319 212 T 730 213 L 11.0
46 319 212 T 731 214 D 15.0
47 319 212 T 734 217 N 14.7
48 320 213 K 561 44 D 15.6
49 320 213 K 563 46 V 0.2
50 320 213 K 564 47 K 0.9
51 320 213 K 636 119 K 10.2
52 322 215 M 563 46 V 23.6
53 322 215 M 726 209 D 6.4
54 322 215 M 727 210 S 5.3
55 322 215 M 730 213 L 18.6

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: 4oqb_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 ++

    4oqb_A: 3 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 60

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


    Query: 147 LERARATTKKIEDLTELEGWEE 168

    R +++ +EL W++

    4oqb_A: 61 GHSIRHPDVEVDGFSELR-WDD 81

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


    Download alignment FASTA file