Interaction between Poly [ADP-ribose] polymerase 1 (4dqy_A) and Poly [ADP-ribose] polymerase 1 (4dqy_B)

PDB and SCOP data

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

Title: Structure of Human PARP-1 bound to a DNA double strand break

Release date: 2012-05-30

Resolution: 3.2 Å

  • Chain A: 4dqy_A

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 116 (30 missing in structure)

  • Chain B: 4dqy_B

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 160 (24 missing in structure)

Buried interface area: 469.94 Å2

Number of inter-residue contacts at the interface: 38

Number of H-bonds: 6

Number of salt bridges: 2

  • Pairwise interaction

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    Download PyMOL visualization script

  • Biological assembly

    Heteromer, 3 proteins, 1 nucleic acid.

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Create a structural model for this interaction

  • Interface residues in 4dqy_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 10 30 R 7.4 12.3 %
    2 13 33 Y 18.8 29.7 %
    3 15 35 K 24.5 17.0 %
    4 30 50 K 13.5 10.5 %
    5 68 88 D 7.1 8.6 %
    6 72 92 D 30.8 55.0 %
    7 73 93 G 6.6 72.5 %
    8 74 94 F 0.2 2.1 %
    9 75 95 S 48.2 57.7 %
    10 76 96 E 77.2 59.6 %
    11 77 97 L 13.5 80.7 %
    12 78 98 R 75.5 48.2 %
    13 79 99 W 128.3 76.6 %
    14 82 102 Q 8.2 31.4 %
    15 86 106 K 10.2 10.1 %

  • Interface residues in 4dqy_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 235 21 E 37.1 27.8 %
    2 238 24 L 22.5 42.1 %
    3 239 25 K 44.1 36.4 %
    4 242 28 N 53.8 71.9 %
    5 243 29 D 8.9 15.9 %
    6 246 32 W 91.6 75.2 %
    7 247 33 N 1.1 1.2 %
    8 249 35 K 1.0 9.2 %
    9 250 36 D 21.5 28.9 %
    10 275 61 G 4.1 10.5 %
    11 276 62 E 14.1 13.9 %
    12 277 63 S 19.8 28.8 %
    13 281 67 D 16.5 25.7 %
    14 304 90 F 24.3 36.3 %
    15 305 91 K 38.7 30.2 %
    16 306 92 S 51.3 66.3 %
    17 358 144 P 16.1 20.8 %
    18 359 145 P 3.2 1.9 %

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 10 30 R 305 91 K 7.4
2 13 33 Y 246 32 W 18.8
3 15 35 K 275 61 G 4.1
4 15 35 K 276 62 E 0.5
5 15 35 K 277 63 S 19.8
6 30 50 K 276 62 E 13.5
7 68 88 D 358 144 P 3.9
8 68 88 D 359 145 P 3.2
9 72 92 D 305 91 K 22.9 H-bond, Salt bridge
10 72 92 D 306 92 S 7.9
11 73 93 G 305 91 K <0.1
12 73 93 G 306 92 S 6.6
13 74 94 F 306 92 S 0.2
14 75 95 S 242 28 N 8.8
15 75 95 S 304 90 F 6.8
16 75 95 S 306 92 S 20.4 H-bond
17 75 95 S 358 144 P 12.2
18 76 96 E 242 28 N 0.9
19 76 96 E 246 32 W 16.7
20 76 96 E 249 35 K 1.0
21 76 96 E 281 67 D 16.5
22 76 96 E 304 90 F 17.6
23 76 96 E 305 91 K 8.4
24 76 96 E 306 92 S 16.2 H-bond
25 77 97 L 242 28 N 6.9 H-bond
26 77 97 L 246 32 W 6.5
27 78 98 R 242 28 N 2.7
28 78 98 R 243 29 D 0.5
29 78 98 R 246 32 W 49.6
30 78 98 R 247 33 N 1.1
31 78 98 R 250 36 D 21.5 H-bond, Salt bridge
32 79 99 W 235 21 E 26.8
33 79 99 W 238 24 L 22.5
34 79 99 W 239 25 K 44.1
35 79 99 W 242 28 N 26.4 H-bond
36 79 99 W 243 29 D 8.5
37 82 102 Q 242 28 N 8.2
38 86 106 K 235 21 E 10.2

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: 4dqy_A; Poly [ADP-ribose] polymerase 1

    Alignment data:

    Expectation value = 3.15e-6, Score = 50 bits (118),

    Identities = 31% (27/88), Positive = 53% (47/88), Gaps = 3% (3/88).

    Interface alignment data:

    Interface residues in alignment: 100% (15/15).

    Identities = 40% (6/15), Positive = 60% (9/15), Gaps = 0% (0/15).

    Query: 87 EMAEQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEK 146

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

    4dqy_A: 23 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 80

    dssp: ---EEEEE------E------E-----EEEEEEEE----- -EEEEEEE--HHHH-


    Query: 147 LERARATTKKIEDLTELEGWEELEDNEK 174

    R +++ +EL W++ + +K

    4dqy_A: 81 GHSIRHPDVEVDGFSELR-WDDQQKVKK 107

    dssp: ------HHHHEE------ HHHHHHHHH


    Download alignment FASTA file