Interaction between Poly [ADP-ribose] polymerase 1 (3oda_H) and Nucleic acid (3oda_O_P)

PDB and SCOP data

PDB ID: 3oda (all binary interactions in this PDB entry)

Title: Human PARP-1 zinc finger 1 (Zn1) bound to DNA

Release date: 2011-01-12

Resolution: 2.6 Å

  • Chain A: 3oda_H

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 116 (28 missing in structure)

  • Chain B: 3oda_O_P

    Title: Nucleic acid

    Number of residues: 20

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

Buried interface area: 468.67 Å2

Number of inter-residue contacts at the interface: 27

Number of H-bonds: 4

  • Pairwise interaction

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    Download PyMOL visualization script

  • Biological assembly

    Homomer, 2 proteins, 1 nucleic acid.

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Create a structural model for this interaction

  • Interface residues in 3oda_H

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 15 35 K 53.3 35.2 %
    2 16 36 S 26.2 71.1 %
    3 18 38 R 111.6 57.0 %
    4 19 39 A 27.8 100.0 %
    5 20 40 S 16.1 29.4 %
    6 22 42 K 27.5 24.2 %
    7 34 54 R 18.9 99.0 %
    8 43 63 M 11.1 6.7 %
    9 44 64 F 70.7 76.7 %
    10 45 65 D 12.4 8.4 %
    11 47 67 K 6.2 9.6 %
    12 48 68 V 31.2 64.5 %
    13 49 69 P 28.4 60.4 %
    14 50 70 H 3.4 5.3 %
    15 51 71 W 24.0 78.8 %

  • Interface residues in 3oda_O_P

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 1 1:O1 G 85.1 37.6 %
    2 4 4:O1 T 4.7 2.5 %
    3 5 5:O1 G 31.3 17.6 %
    4 6 6:O1 C 11.3 7.0 %
    5 17 7:P1 A 7.7 4.4 %
    6 18 8:P1 G 90.7 45.6 %
    7 19 9:P1 G 97.2 63.0 %
    8 20 10:P1 C 140.6 53.2 %

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 15 35 K 18 8:P1 G 48.1
2 15 35 K 19 9:P1 G 5.2
3 16 36 S 18 8:P1 G 12.6
4 16 36 S 19 9:P1 G 13.6 H-bond
5 18 38 R 4 4:O1 T 4.7
6 18 38 R 5 5:O1 G 31.3
7 18 38 R 6 6:O1 C 11.3
8 18 38 R 17 7:P1 A 7.7
9 18 38 R 18 8:P1 G 30.0
10 18 38 R 19 9:P1 G 24.8
11 18 38 R 20 10:P1 C 1.7
12 19 39 A 19 9:P1 G 20.0
13 19 39 A 20 10:P1 C 7.8
14 20 40 S 20 10:P1 C 16.1 H-bond
15 22 42 K 20 10:P1 C 27.5 H-bond
16 34 54 R 19 9:P1 G 18.9 H-bond
17 43 63 M 1 1:O1 G 11.1
18 44 64 F 1 1:O1 G 61.6
19 44 64 F 20 10:P1 C 9.0
20 45 65 D 1 1:O1 G 12.4
21 47 67 K 20 10:P1 C 6.2
22 48 68 V 20 10:P1 C 31.2
23 49 69 P 19 9:P1 G 2.4
24 49 69 P 20 10:P1 C 26.0
25 50 70 H 20 10:P1 C 3.4
26 51 71 W 19 9:P1 G 12.3
27 51 71 W 20 10:P1 C 11.7

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: 3oda_H; 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 = 33% (5/15), Positive = 47% (7/15), Gaps = 0% (0/15).

    Query: 87 EMAEQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEK 146

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

    3oda_H: 23 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 80

    dssp: ----EEEEE------E------E-----EEEEEEEE----- -EEEEEEEHHHHH--


    Query: 147 LERARATTKKIEDLTELEGWEELEDNEK 174

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

    3oda_H: 81 GHSIRHPDVEVDGFSELR-WDDQQKVKK 107

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


    Download alignment FASTA file