Interaction between Poly [ADP-ribose] polymerase 1 (4oqb_D) and Poly [ADP-ribose] polymerase 1 (4oqb_F)

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_D

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 267 (45 missing in structure)

  • Chain B: 4oqb_F

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 505 (49 missing in structure)

Buried interface area: 702.73 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 4oqb_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 40 40 Q 40.9 43.9 %
    2 41 41 S 6.6 46.3 %
    3 42 42 P 32.9 26.6 %
    4 43 43 M 54.8 33.0 %
    5 44 44 F 31.0 26.0 %
    6 45 45 D 89.9 80.4 %
    7 46 46 G 0.9 4.8 %
    8 314 207 D 32.6 36.7 %
    9 315 208 V 21.3 24.3 %
    10 316 209 T 19.4 31.2 %
    11 317 210 A 59.0 65.4 %
    12 318 211 W 180.7 83.1 %
    13 319 212 T 50.6 87.9 %
    14 320 213 K 24.2 19.8 %
    15 322 215 M 57.9 34.0 %

  • Interface residues in 4oqb_F

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 559 42 L 2.8 14.7 %
    2 560 43 V 6.3 69.7 %
    3 561 44 D 19.4 59.4 %
    4 563 46 V 21.9 20.7 %
    5 566 49 T 20.4 56.5 %
    6 567 50 N 7.3 67.1 %
    7 568 51 S 18.1 56.6 %
    8 589 72 W 32.7 34.1 %
    9 590 73 G 12.4 86.8 %
    10 591 74 R 33.0 73.0 %
    11 595 78 V 2.0 1.4 %
    12 596 79 I 58.7 71.8 %
    13 597 80 G 28.2 61.7 %
    14 598 81 S 28.5 49.5 %
    15 633 116 K 74.3 82.8 %
    16 634 117 Y 4.7 4.7 %
    17 635 118 P 52.5 46.6 %
    18 636 119 K 12.0 11.1 %
    19 639 122 Y 27.0 49.5 %
    20 726 209 D 6.9 5.9 %
    21 727 210 S 39.1 50.0 %
    22 730 213 L 28.0 67.3 %
    23 731 214 D 45.9 69.2 %
    24 734 217 N 29.8 97.7 %
    25 735 218 R 51.8 47.0 %
    26 738 221 T 18.8 80.5 %
    27 739 222 L 4.5 84.8 %
    28 746 229 M 15.7 12.4 %

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 4.3
2 40 40 Q 596 79 I 20.9
3 40 40 Q 746 229 M 15.7
4 41 41 S 596 79 I 6.6
5 42 42 P 595 78 V 2.0
6 42 42 P 596 79 I 17.3
7 42 42 P 597 80 G 13.6 H-bond
8 43 43 M 589 72 W 15.7 H-bond
9 43 43 M 597 80 G 10.5
10 43 43 M 598 81 S 28.5
11 44 44 F 589 72 W 16.9
12 44 44 F 590 73 G 2.7
13 44 44 F 596 79 I 7.4
14 44 44 F 597 80 G 4.1
15 45 45 D 566 49 T 19.5 H-bond
16 45 45 D 567 50 N 7.3 H-bond
17 45 45 D 568 51 S 18.1 H-bond
18 45 45 D 589 72 W 0.1
19 45 45 D 590 73 G 9.7
20 45 45 D 591 74 R 28.7 H-bond, Salt bridge
21 45 45 D 596 79 I 6.4
22 46 46 G 566 49 T 0.9
23 314 207 D 635 118 P 32.2
24 314 207 D 636 119 K 0.3
25 315 208 V 727 210 S 21.3
26 316 209 T 635 118 P 0.2
27 316 209 T 727 210 S 1.2
28 316 209 T 731 214 D 18.0
29 317 210 A 633 116 K 32.2
30 317 210 A 634 117 Y 4.7
31 317 210 A 635 118 P 20.1
32 317 210 A 636 119 K 2.1
33 318 211 W 559 42 L 2.8
34 318 211 W 560 43 V 6.3
35 318 211 W 561 44 D 2.6
36 318 211 W 633 116 K 42.2
37 318 211 W 639 122 Y 27.0
38 318 211 W 731 214 D 10.9
39 318 211 W 734 217 N 13.8
40 318 211 W 735 218 R 51.8
41 318 211 W 738 221 T 18.8
42 318 211 W 739 222 L 4.5
43 319 212 T 561 44 D 2.9
44 319 212 T 727 210 S 6.3
45 319 212 T 730 213 L 8.5
46 319 212 T 731 214 D 17.0
47 319 212 T 734 217 N 15.9
48 320 213 K 561 44 D 13.9
49 320 213 K 636 119 K 9.6
50 320 213 K 727 210 S 0.7
51 322 215 M 563 46 V 21.9
52 322 215 M 726 209 D 6.9
53 322 215 M 727 210 S 9.6
54 322 215 M 730 213 L 19.5

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_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: 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_D: 3 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 60

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


    Query: 147 LERARATTKKIEDLTELEGWEE 168

    R +++ +EL W++

    4oqb_D: 61 GHSIRHPDVEVDGFSELR-WDD 81

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


    Download alignment FASTA file