Interaction between Poly [ADP-ribose] polymerase 1 (4dqy_D) and Poly [ADP-ribose] polymerase 1 (4dqy_E)

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_D

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 116 (30 missing in structure)

  • Chain B: 4dqy_E

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 160 (24 missing in structure)

Buried interface area: 433.88 Å2

Number of inter-residue contacts at the interface: 32

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_D

    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 17.8 28.1 %
    3 15 35 K 19.3 13.3 %
    4 30 50 K 12.5 9.6 %
    5 68 88 D 0.5 0.6 %
    6 72 92 D 29.4 51.0 %
    7 73 93 G 5.6 63.8 %
    8 75 95 S 45.5 54.1 %
    9 76 96 E 72.6 56.5 %
    10 77 97 L 12.4 79.3 %
    11 78 98 R 70.4 44.7 %
    12 79 99 W 124.3 72.3 %
    13 82 102 Q 7.4 29.5 %
    14 86 106 K 8.7 8.5 %

  • Interface residues in 4dqy_E

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 235 21 E 37.0 28.2 %
    2 238 24 L 19.6 37.4 %
    3 239 25 K 44.3 37.1 %
    4 242 28 N 53.2 69.4 %
    5 243 29 D 7.0 12.7 %
    6 246 32 W 88.0 71.2 %
    7 250 36 D 20.1 26.8 %
    8 275 61 G 1.2 3.0 %
    9 276 62 E 12.5 12.2 %
    10 277 63 S 18.1 25.9 %
    11 281 67 D 13.0 19.9 %
    12 304 90 F 20.4 30.7 %
    13 305 91 K 35.1 27.3 %
    14 306 92 S 51.2 66.2 %
    15 358 144 P 12.8 16.8 %
    16 359 145 P 0.5 0.3 %

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 7.3
2 10 30 R 306 92 S <0.1
3 13 33 Y 246 32 W 17.8
4 15 35 K 275 61 G 1.2
5 15 35 K 277 63 S 18.1
6 30 50 K 276 62 E 12.5
7 68 88 D 359 145 P 0.5
8 72 92 D 305 91 K 20.8 Salt bridge
9 72 92 D 306 92 S 8.6
10 73 93 G 306 92 S 5.6
11 75 95 S 242 28 N 9.4
12 75 95 S 304 90 F 4.4
13 75 95 S 306 92 S 18.9 H-bond
14 75 95 S 358 144 P 12.8
15 76 96 E 242 28 N 1.5
16 76 96 E 246 32 W 17.2 H-bond
17 76 96 E 281 67 D 13.0
18 76 96 E 304 90 F 16.0
19 76 96 E 305 91 K 7.0
20 76 96 E 306 92 S 18.0 H-bond
21 77 97 L 242 28 N 7.0 H-bond
22 77 97 L 246 32 W 5.4
23 78 98 R 242 28 N 2.9
24 78 98 R 246 32 W 47.5
25 78 98 R 250 36 D 20.1 H-bond, Salt bridge
26 79 99 W 235 21 E 28.4
27 79 99 W 238 24 L 19.6
28 79 99 W 239 25 K 44.3
29 79 99 W 242 28 N 25.0 H-bond
30 79 99 W 243 29 D 7.0
31 82 102 Q 242 28 N 7.4
32 86 106 K 235 21 E 8.7

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: 4dqy_D; 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% (14/14).

    Identities = 43% (6/14), Positive = 64% (9/14), Gaps = 0% (0/14).

    Query: 87 EMAEQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEK 146

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

    4dqy_D: 23 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 80

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


    Query: 147 LERARATTKKIEDLTELEGWEELEDNEK 174

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

    4dqy_D: 81 GHSIRHPDVEVDGFSELR-WDDQQKVKK 107

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


    Download alignment FASTA file