Interaction between Poly [ADP-ribose] polymerase 1 (4opx_A) and Poly [ADP-ribose] polymerase 1 (4opx_C)

PDB and SCOP data

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

Title: Structure of Human PARP-1 bound to a DNA double strand break in complex with (2R)-5-fluoro-2-methyl-2,3-dihydro-1-benzofuran-7-carboxamide

Release date: 2014-07-02

Resolution: 3.3 Å

  • Chain A: 4opx_A

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 267 (45 missing in structure)

  • Chain B: 4opx_C

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 505 (49 missing in structure)

Buried interface area: 706.59 Å2

Number of inter-residue contacts at the interface: 56

Number of H-bonds: 7

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 4opx_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 40 40 Q 45.2 48.4 %
    2 41 41 S 7.3 48.8 %
    3 42 42 P 34.2 27.7 %
    4 43 43 M 55.0 33.2 %
    5 44 44 F 31.5 26.5 %
    6 45 45 D 89.6 81.7 %
    7 46 46 G 0.9 5.0 %
    8 314 207 D 30.3 33.3 %
    9 315 208 V 22.6 25.8 %
    10 316 209 T 21.4 34.3 %
    11 317 210 A 60.1 66.4 %
    12 318 211 W 183.3 83.8 %
    13 319 212 T 51.8 89.9 %
    14 320 213 K 21.0 17.1 %
    15 322 215 M 52.4 30.7 %

  • Interface residues in 4opx_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 559 42 L 2.7 14.2 %
    2 560 43 V 6.3 70.6 %
    3 561 44 D 23.9 73.3 %
    4 563 46 V 24.6 23.3 %
    5 564 47 K 0.1 0.1 %
    6 566 49 T 19.9 55.1 %
    7 567 50 N 7.7 67.3 %
    8 568 51 S 17.8 55.1 %
    9 589 72 W 30.8 32.4 %
    10 590 73 G 12.3 85.6 %
    11 591 74 R 34.9 76.4 %
    12 595 78 V 3.0 2.0 %
    13 596 79 I 61.4 76.9 %
    14 597 80 G 28.7 63.0 %
    15 598 81 S 28.1 48.9 %
    16 633 116 K 73.7 80.2 %
    17 634 117 Y 4.5 4.5 %
    18 635 118 P 52.7 46.9 %
    19 636 119 K 9.1 8.4 %
    20 639 122 Y 24.5 46.1 %
    21 726 209 D 6.4 5.5 %
    22 727 210 S 37.2 48.9 %
    23 730 213 L 30.5 71.7 %
    24 731 214 D 45.7 68.3 %
    25 734 217 N 30.5 99.6 %
    26 735 218 R 48.4 44.4 %
    27 738 221 T 19.0 82.7 %
    28 739 222 L 3.1 76.2 %
    29 746 229 M 19.1 15.2 %

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 4.9
2 40 40 Q 596 79 I 21.2
3 40 40 Q 746 229 M 19.1
4 41 41 S 596 79 I 7.3
5 42 42 P 595 78 V 3.0
6 42 42 P 596 79 I 18.4
7 42 42 P 597 80 G 12.7 H-bond
8 43 43 M 589 72 W 14.9 H-bond
9 43 43 M 597 80 G 12.0
10 43 43 M 598 81 S 28.1
11 44 44 F 589 72 W 15.9
12 44 44 F 590 73 G 3.1
13 44 44 F 596 79 I 8.5
14 44 44 F 597 80 G 4.0
15 45 45 D 566 49 T 19.1 H-bond
16 45 45 D 567 50 N 7.7 H-bond
17 45 45 D 568 51 S 17.8 H-bond
18 45 45 D 589 72 W <0.1
19 45 45 D 590 73 G 9.1
20 45 45 D 591 74 R 30.0 H-bond, Salt bridge
21 45 45 D 596 79 I 6.0
22 46 46 G 566 49 T 0.9
23 314 207 D 635 118 P 29.6
24 314 207 D 636 119 K 0.7
25 315 208 V 727 210 S 22.6
26 316 209 T 635 118 P 0.3
27 316 209 T 727 210 S 3.6
28 316 209 T 731 214 D 17.5 H-bond
29 317 210 A 633 116 K 29.8
30 317 210 A 634 117 Y 4.5
31 317 210 A 635 118 P 22.8
32 317 210 A 636 119 K 3.0
33 318 211 W 559 42 L 2.7
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 43.9
37 318 211 W 639 122 Y 24.5
38 318 211 W 731 214 D 14.1
39 318 211 W 734 217 N 16.3
40 318 211 W 735 218 R 48.4
41 318 211 W 738 221 T 19.0
42 318 211 W 739 222 L 3.1
43 319 212 T 561 44 D 4.0
44 319 212 T 563 46 V 0.1
45 319 212 T 727 210 S 7.0
46 319 212 T 730 213 L 12.4
47 319 212 T 731 214 D 14.1
48 319 212 T 734 217 N 14.2
49 320 213 K 561 44 D 14.8
50 320 213 K 563 46 V 0.7
51 320 213 K 564 47 K 0.1
52 320 213 K 636 119 K 5.4
53 322 215 M 563 46 V 23.8
54 322 215 M 726 209 D 6.4
55 322 215 M 727 210 S 4.0
56 322 215 M 730 213 L 18.1

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: 4opx_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 ++

    4opx_A: 3 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 60

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


    Query: 147 LERARATTKKIEDLTELEGWEE 168

    R +++ +EL W++

    4opx_A: 61 GHSIRHPDVEVDGFSELR-WDD 81

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


    Download alignment FASTA file