Interaction between Poly [ADP-ribose] polymerase 1 (3oda_G) 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_G

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 116 (29 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: 492.59 Å2

Number of inter-residue contacts at the interface: 31

Number of H-bonds: 7

  • Pairwise interaction

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  • Biological assembly

    Homomer, 2 proteins, 1 nucleic acid.

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Create a structural model for this interaction

  • Interface residues in 3oda_G

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 12 32 E 0.3 2.0 %
    2 15 35 K 49.7 33.8 %
    3 16 36 S 26.4 77.7 %
    4 18 38 R 115.3 61.6 %
    5 19 39 A 26.8 100.0 %
    6 20 40 S 21.2 32.2 %
    7 22 42 K 28.8 26.4 %
    8 34 54 R 19.8 100.0 %
    9 41 61 S 1.6 9.2 %
    10 43 63 M 49.6 31.1 %
    11 44 64 F 57.7 54.2 %
    12 47 67 K <0.1 0.1 %
    13 48 68 V 34.3 87.5 %
    14 49 69 P 24.9 51.1 %
    15 50 70 H 9.3 14.3 %
    16 51 71 W 26.9 81.8 %

  • Interface residues in 3oda_O_P

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 7 7:O1 A 6.9 3.9 %
    2 8 8:O1 G 79.8 42.1 %
    3 9 9:O1 G 96.5 62.4 %
    4 10 10:O1 C 154.0 59.1 %
    5 11 1:P1 G 91.5 40.6 %
    6 12 2:P1 C 4.4 2.5 %
    7 14 4:P1 T 4.5 2.5 %
    8 15 5:P1 G 35.4 20.1 %
    9 16 6:P1 C 19.8 12.6 %

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:O1 G 0.3
2 15 35 K 8 8:O1 G 41.6
3 15 35 K 9 9:O1 G 8.1
4 16 36 S 8 8:O1 G 12.3 H-bond
5 16 36 S 9 9:O1 G 14.1 H-bond
6 18 38 R 7 7:O1 A 6.9
7 18 38 R 8 8:O1 G 25.8
8 18 38 R 9 9:O1 G 21.3
9 18 38 R 10 10:O1 C 1.7
10 18 38 R 14 4:P1 T 4.5 H-bond
11 18 38 R 15 5:P1 G 35.4 H-bond
12 18 38 R 16 6:P1 C 19.8
13 19 39 A 9 9:O1 G 18.7
14 19 39 A 10 10:O1 C 8.1
15 20 40 S 10 10:O1 C 21.2 H-bond
16 22 42 K 10 10:O1 C 28.8 H-bond
17 34 54 R 9 9:O1 G 19.8 H-bond
18 41 61 S 10 10:O1 C 1.6
19 41 61 S 11 1:P1 G <0.1
20 43 63 M 10 10:O1 C 3.7
21 43 63 M 11 1:P1 G 41.6
22 43 63 M 12 2:P1 C 4.4
23 44 64 F 10 10:O1 C 7.8
24 44 64 F 11 1:P1 G 49.9
25 47 67 K 10 10:O1 C <0.1
26 48 68 V 10 10:O1 C 34.3
27 49 69 P 9 9:O1 G 0.9
28 49 69 P 10 10:O1 C 24.0
29 50 70 H 10 10:O1 C 9.3
30 51 71 W 9 9:O1 G 13.4
31 51 71 W 10 10:O1 C 13.5

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_G; 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_G: 23 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 80

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


    Query: 147 LERARATTKKIEDLTELEGWEELEDNEK 174

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

    3oda_G: 81 GHSIRHPDVEVDGFSELR-WDDQQKVKK 107

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


    Download alignment FASTA file