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

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_A

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 116 (29 missing in structure)

  • Chain B: 3oda_I_J

    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: 466.92 Å2

Number of inter-residue contacts at the interface: 29

Number of H-bonds: 5

  • 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_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 12 32 E <0.1 0.4 %
    2 15 35 K 53.0 36.0 %
    3 16 36 S 26.8 70.5 %
    4 18 38 R 116.8 61.2 %
    5 19 39 A 26.6 100.0 %
    6 20 40 S 22.0 33.8 %
    7 22 42 K 28.2 25.7 %
    8 34 54 R 19.8 99.8 %
    9 43 63 M 5.6 3.6 %
    10 44 64 F 67.3 74.6 %
    11 45 65 D 8.0 5.6 %
    12 47 67 K 1.5 2.0 %
    13 48 68 V 34.6 85.7 %
    14 49 69 P 23.2 47.8 %
    15 50 70 H 8.2 12.7 %
    16 51 71 W 25.2 77.0 %

  • Interface residues in 3oda_I_J

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 7 7:I1 A 7.0 4.0 %
    2 8 8:I1 G 87.7 45.7 %
    3 9 9:I1 G 95.8 62.1 %
    4 10 10:I1 C 149.4 56.8 %
    5 11 1:J1 G 72.4 30.1 %
    6 14 4:J1 T 4.8 2.5 %
    7 15 5:J1 G 35.0 22.0 %
    8 16 6:J1 C 14.8 9.0 %

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 9 9:I1 G <0.1
2 15 35 K 8 8:I1 G 46.2
3 15 35 K 9 9:I1 G 6.8
4 16 36 S 8 8:I1 G 12.1 H-bond
5 16 36 S 9 9:I1 G 14.7 H-bond
6 18 38 R 7 7:I1 A 7.0
7 18 38 R 8 8:I1 G 29.4
8 18 38 R 9 9:I1 G 23.5
9 18 38 R 10 10:I1 C 2.3
10 18 38 R 14 4:J1 T 4.8
11 18 38 R 15 5:J1 G 35.0
12 18 38 R 16 6:J1 C 14.8
13 19 39 A 9 9:I1 G 18.4
14 19 39 A 10 10:I1 C 8.2
15 20 40 S 10 10:I1 C 22.0 H-bond
16 22 42 K 10 10:I1 C 28.2 H-bond
17 34 54 R 9 9:I1 G 19.8 H-bond
18 43 63 M 11 1:J1 G 5.6
19 44 64 F 10 10:I1 C 8.8
20 44 64 F 11 1:J1 G 58.5
21 45 65 D 11 1:J1 G 8.0
22 47 67 K 10 10:I1 C 1.5
23 48 68 V 10 10:I1 C 34.3
24 48 68 V 11 1:J1 G 0.3
25 49 69 P 9 9:I1 G <0.1
26 49 69 P 10 10:I1 C 23.2
27 50 70 H 10 10:I1 C 8.2
28 51 71 W 9 9:I1 G 12.5
29 51 71 W 10 10:I1 C 12.7

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_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% (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 ++

    3oda_A: 23 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 80

    dssp: ----EEEEE------E------E-----EEEEEEEE----- -EEEEEEEHHHHHH-


    Query: 147 LERARATTKKIEDLTELEGWEELEDNEK 174

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

    3oda_A: 81 GHSIRHPDVEVDGFSELR-WDDQQKVKK 107

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


    Download alignment FASTA file