Interaction between Poly [ADP-ribose] polymerase 1 (4opx_D) and Poly [ADP-ribose] polymerase 1 (4opx_F)

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_D

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 267 (45 missing in structure)

  • Chain B: 4opx_F

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 505 (49 missing in structure)

Buried interface area: 700.04 Å2

Number of inter-residue contacts at the interface: 53

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_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 40 40 Q 41.0 43.7 %
    2 41 41 S 6.7 46.2 %
    3 42 42 P 34.0 27.4 %
    4 43 43 M 54.9 33.2 %
    5 44 44 F 30.3 25.5 %
    6 45 45 D 90.0 81.9 %
    7 46 46 G 1.3 7.1 %
    8 314 207 D 30.7 34.1 %
    9 315 208 V 22.0 25.2 %
    10 316 209 T 20.1 32.5 %
    11 317 210 A 58.8 64.5 %
    12 318 211 W 180.9 83.0 %
    13 319 212 T 50.8 88.7 %
    14 320 213 K 19.6 15.9 %
    15 322 215 M 59.0 34.9 %

  • Interface residues in 4opx_F

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 559 42 L 2.5 13.0 %
    2 560 43 V 6.0 67.8 %
    3 561 44 D 18.8 57.4 %
    4 563 46 V 21.2 20.0 %
    5 566 49 T 22.0 60.9 %
    6 567 50 N 7.7 67.1 %
    7 568 51 S 17.5 54.7 %
    8 589 72 W 30.9 32.4 %
    9 590 73 G 11.9 84.5 %
    10 591 74 R 34.2 76.3 %
    11 595 78 V 2.0 1.3 %
    12 596 79 I 59.5 73.4 %
    13 597 80 G 28.0 61.4 %
    14 598 81 S 27.2 47.2 %
    15 633 116 K 74.7 82.1 %
    16 634 117 Y 4.2 4.2 %
    17 635 118 P 51.7 45.6 %
    18 636 119 K 7.2 6.7 %
    19 639 122 Y 26.4 49.1 %
    20 726 209 D 8.1 6.9 %
    21 727 210 S 41.2 53.4 %
    22 730 213 L 29.1 69.5 %
    23 731 214 D 46.4 70.4 %
    24 734 217 N 30.1 97.6 %
    25 735 218 R 51.3 46.7 %
    26 738 221 T 18.8 80.9 %
    27 739 222 L 4.1 83.6 %
    28 746 229 M 17.2 13.7 %

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 4.6
2 40 40 Q 596 79 I 19.2
3 40 40 Q 746 229 M 17.2
4 41 41 S 596 79 I 6.7
5 42 42 P 595 78 V 2.0
6 42 42 P 596 79 I 19.3
7 42 42 P 597 80 G 12.7 H-bond
8 43 43 M 589 72 W 15.8 H-bond
9 43 43 M 597 80 G 11.9
10 43 43 M 598 81 S 27.2
11 44 44 F 589 72 W 15.1
12 44 44 F 590 73 G 3.4
13 44 44 F 596 79 I 8.4
14 44 44 F 597 80 G 3.4
15 45 45 D 566 49 T 20.8 H-bond
16 45 45 D 567 50 N 7.7 H-bond
17 45 45 D 568 51 S 17.5 H-bond
18 45 45 D 590 73 G 8.5
19 45 45 D 591 74 R 29.7 H-bond, Salt bridge
20 45 45 D 596 79 I 5.9
21 46 46 G 566 49 T 1.3
22 314 207 D 635 118 P 30.7
23 314 207 D 636 119 K <0.1
24 315 208 V 727 210 S 22.0
25 316 209 T 635 118 P 0.1
26 316 209 T 727 210 S 1.4
27 316 209 T 731 214 D 18.6 H-bond
28 317 210 A 633 116 K 31.7
29 317 210 A 634 117 Y 4.2
30 317 210 A 635 118 P 20.9
31 317 210 A 636 119 K 1.9
32 318 211 W 559 42 L 2.5
33 318 211 W 560 43 V 6.0
34 318 211 W 561 44 D 3.1
35 318 211 W 633 116 K 43.0
36 318 211 W 639 122 Y 26.4
37 318 211 W 731 214 D 11.3
38 318 211 W 734 217 N 14.4
39 318 211 W 735 218 R 51.3
40 318 211 W 738 221 T 18.8
41 318 211 W 739 222 L 4.1
42 319 212 T 561 44 D 2.5
43 319 212 T 727 210 S 6.6
44 319 212 T 730 213 L 9.5
45 319 212 T 731 214 D 16.5
46 319 212 T 734 217 N 15.7
47 320 213 K 561 44 D 13.2
48 320 213 K 636 119 K 5.3
49 320 213 K 727 210 S 1.1
50 322 215 M 563 46 V 21.2
51 322 215 M 726 209 D 8.1
52 322 215 M 727 210 S 10.1
53 322 215 M 730 213 L 19.7

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: 4opx_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 ++

    4opx_D: 3 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 60

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


    Query: 147 LERARATTKKIEDLTELEGWEE 168

    R +++ +EL W++

    4opx_D: 61 GHSIRHPDVEVDGFSELR-WDD 81

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


    Download alignment FASTA file