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

    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: 445.81 Å2

Number of inter-residue contacts at the interface: 29

Number of H-bonds: 4

  • 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 12 32 E <0.1 0.5 %
    2 15 35 K 51.4 34.7 %
    3 16 36 S 27.8 69.4 %
    4 18 38 R 104.1 54.8 %
    5 19 39 A 36.5 98.1 %
    6 20 40 S 23.6 35.8 %
    7 22 42 K 20.7 20.6 %
    8 34 54 R 17.4 99.9 %
    9 41 61 S <0.1 0.6 %
    10 43 63 M 18.4 10.4 %
    11 44 64 F 68.6 65.2 %
    12 47 67 K 0.1 0.1 %
    13 48 68 V 34.5 85.7 %
    14 49 69 P 16.2 33.4 %
    15 50 70 H 0.6 1.4 %
    16 51 71 W 25.7 71.7 %

  • Interface residues in 4dqy_M_N

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 23 23:M1 A 6.7 3.6 %
    2 24 24:M1 G 85.7 43.0 %
    3 25 25:M1 G 98.0 63.5 %
    4 26 26:M1 C 129.6 48.3 %
    5 27 1:N1 G 74.9 30.7 %
    6 30 4:N1 T 2.8 1.4 %
    7 31 5:N1 A 34.1 18.4 %
    8 32 6:N1 C 14.0 8.1 %

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 25 25:M1 G <0.1
2 15 35 K 24 24:M1 G 46.7
3 15 35 K 25 25:M1 G 4.7
4 16 36 S 24 24:M1 G 12.2 H-bond
5 16 36 S 25 25:M1 G 15.6 H-bond
6 18 38 R 23 23:M1 A 6.7
7 18 38 R 24 24:M1 G 26.8
8 18 38 R 25 25:M1 G 19.7
9 18 38 R 30 4:N1 T 2.8
10 18 38 R 31 5:N1 A 34.1
11 18 38 R 32 6:N1 C 14.0
12 19 39 A 25 25:M1 G 26.2
13 19 39 A 26 26:M1 C 10.4
14 20 40 S 26 26:M1 C 23.6 H-bond
15 22 42 K 26 26:M1 C 20.7
16 34 54 R 25 25:M1 G 17.4 H-bond
17 41 61 S 26 26:M1 C <0.1
18 41 61 S 27 1:N1 G <0.1
19 43 63 M 26 26:M1 C 2.0
20 43 63 M 27 1:N1 G 16.4
21 44 64 F 26 26:M1 C 10.1
22 44 64 F 27 1:N1 G 58.5
23 47 67 K 26 26:M1 C 0.1
24 48 68 V 26 26:M1 C 34.5
25 49 69 P 25 25:M1 G 2.0
26 49 69 P 26 26:M1 C 14.2
27 50 70 H 26 26:M1 C 0.6
28 51 71 W 25 25:M1 G 12.3
29 51 71 W 26 26:M1 C 13.4

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% (16/16).

    Identities = 31% (5/16), Positive = 50% (8/16), Gaps = 0% (0/16).

    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