Interaction between Poly [ADP-ribose] polymerase 1 (3od8_G) and Nucleic acid (3od8_O_P)

PDB and SCOP data

PDB ID: 3od8 (all binary interactions in this PDB entry)

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

Release date: 2011-01-12

Resolution: 2.4 Å

  • Chain A: 3od8_G

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 116 (29 missing in structure)

  • Chain B: 3od8_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: 486.64 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

    Homomer, 2 proteins, 1 nucleic acid.

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Create a structural model for this interaction

  • Interface residues in 3od8_G

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 12 32 E <0.1 0.0 %
    2 15 35 K 48.8 30.8 %
    3 16 36 S 26.5 80.5 %
    4 18 38 R 116.8 62.5 %
    5 19 39 A 25.5 100.0 %
    6 20 40 S 23.1 33.4 %
    7 22 42 K 29.8 26.6 %
    8 34 54 R 18.8 99.1 %
    9 41 61 S 2.3 14.8 %
    10 43 63 MSE 34.3 20.1 %
    11 44 64 F 62.3 65.4 %
    12 48 68 V 32.5 88.6 %
    13 49 69 P 29.8 54.8 %
    14 50 70 H 10.7 17.3 %
    15 51 71 W 25.4 86.0 %

  • Interface residues in 3od8_O_P

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 7 7:O1 T 2.8 1.5 %
    2 8 8:O1 G 79.3 42.0 %
    3 9 9:O1 G 98.3 63.9 %
    4 10 10:O1 G 170.8 62.1 %
    5 11 1:P1 C 63.6 30.9 %
    6 12 2:P1 C 10.2 6.2 %
    7 14 4:P1 A 3.3 2.1 %
    8 15 5:P1 A 31.1 17.7 %
    9 16 6:P1 G 27.2 15.8 %

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 9 9:O1 G <0.1
2 15 35 K 8 8:O1 G 39.9
3 15 35 K 9 9:O1 G 8.9
4 16 36 S 8 8:O1 G 11.4
5 16 36 S 9 9:O1 G 15.1 H-bond
6 18 38 R 7 7:O1 T 2.8
7 18 38 R 8 8:O1 G 28.0
8 18 38 R 9 9:O1 G 22.5
9 18 38 R 10 10:O1 G 1.9
10 18 38 R 14 4:P1 A 3.3
11 18 38 R 15 5:P1 A 31.1
12 18 38 R 16 6:P1 G 27.2
13 19 39 A 9 9:O1 G 17.7
14 19 39 A 10 10:O1 G 7.8
15 20 40 S 10 10:O1 G 23.1 H-bond
16 22 42 K 10 10:O1 G 29.8 H-bond
17 34 54 R 9 9:O1 G 18.8 H-bond
18 41 61 S 10 10:O1 G 2.3
19 43 63 MSE 10 10:O1 G 10.6
20 43 63 MSE 11 1:P1 C 13.5
21 43 63 MSE 12 2:P1 C 10.2
22 44 64 F 10 10:O1 G 12.2
23 44 64 F 11 1:P1 C 50.1
24 48 68 V 10 10:O1 G 32.5
25 49 69 P 9 9:O1 G 2.6
26 49 69 P 10 10:O1 G 27.2
27 50 70 H 10 10:O1 G 10.7
28 51 71 W 9 9:O1 G 12.7
29 51 71 W 10 10:O1 G 12.8

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: 3od8_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% (15/15).

    Identities = 33% (5/15), Positive = 53% (8/15), Gaps = 0% (0/15).

    Query: 87 EMAEQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEK 146

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

    3od8_G: 23 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 80

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


    Query: 147 LERARATTKKIEDLTELEGWEELEDNEK 174

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

    3od8_G: 81 GHSIRHPDVEVDGFSELR-WDDQQKVKK 107

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


    Download alignment FASTA file