Interaction between Poly [ADP-ribose] polymerase 1 (4dqy_A) and DNA (26-MER) (4dqy_M_N)

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_M_N

    Title: DNA (26-MER)

    Number of residues: 52

    Note: Residues of nucleic acid domain are renumbered to avoid repeating the same residue numbers from different PDB chains.

Buried interface area: 470.57 Å2

Number of inter-residue contacts at the interface: 30

Number of H-bonds: 4

  • Pairwise interaction

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  • 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 12 32 E 0.5 2.9 %
    2 15 35 K 60.2 41.2 %
    3 16 36 S 30.1 73.5 %
    4 18 38 R 115.8 65.1 %
    5 19 39 A 34.6 96.5 %
    6 20 40 S 21.0 32.0 %
    7 22 42 K 19.0 18.9 %
    8 30 50 K 4.7 3.6 %
    9 34 54 R 17.5 100.0 %
    10 41 61 S 0.1 1.1 %
    11 43 63 M 14.7 8.3 %
    12 44 64 F 68.6 65.1 %
    13 47 67 K 0.7 0.5 %
    14 48 68 V 34.8 88.4 %
    15 49 69 P 21.2 42.6 %
    16 50 70 H 0.6 1.2 %
    17 51 71 W 26.3 76.3 %

  • Interface residues in 4dqy_M_N

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 1 1:M1 G 72.9 31.5 %
    2 4 4:M1 T 3.3 1.8 %
    3 5 5:M1 A 39.1 21.8 %
    4 6 6:M1 C 23.2 13.1 %
    5 7 7:M1 C 4.7 2.8 %
    6 49 23:N1 A 9.6 5.1 %
    7 50 24:N1 G 90.4 47.5 %
    8 51 25:N1 G 98.4 64.4 %
    9 52 26:N1 C 129.0 47.8 %

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. of chain B in PDB Residue in chain B Contact area, Å2 Contact type
1 12 32 E 51 25:N1 G 0.5
2 15 35 K 50 24:N1 G 52.3
3 15 35 K 51 25:N1 G 8.0
4 16 36 S 6 6:M1 C 1.3
5 16 36 S 50 24:N1 G 13.4 H-bond
6 16 36 S 51 25:N1 G 15.4 H-bond
7 18 38 R 4 4:M1 T 3.3
8 18 38 R 5 5:M1 A 39.1
9 18 38 R 6 6:M1 C 21.9
10 18 38 R 49 23:N1 A 9.6
11 18 38 R 50 24:N1 G 24.7
12 18 38 R 51 25:N1 G 17.3
13 19 39 A 51 25:N1 G 23.5
14 19 39 A 52 26:N1 C 11.1
15 20 40 S 52 26:N1 C 21.0 H-bond
16 22 42 K 52 26:N1 C 19.0
17 30 50 K 7 7:M1 C 4.7
18 34 54 R 51 25:N1 G 17.5 H-bond
19 41 61 S 1 1:M1 G 0.1
20 43 63 M 1 1:M1 G 14.4
21 43 63 M 52 26:N1 C 0.3
22 44 64 F 1 1:M1 G 58.4
23 44 64 F 52 26:N1 C 10.2
24 47 67 K 52 26:N1 C 0.7
25 48 68 V 52 26:N1 C 34.8
26 49 69 P 51 25:N1 G 3.0
27 49 69 P 52 26:N1 C 18.2
28 50 70 H 52 26:N1 C 0.6
29 51 71 W 51 25:N1 G 13.2
30 51 71 W 52 26:N1 C 13.1

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: 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% (17/17).

    Identities = 35% (6/17), Positive = 53% (9/17), Gaps = 0% (0/17).

    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