Interaction between Poly [ADP-ribose] polymerase 1 (3od8_E) and Nucleic acid (3od8_M_N)

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_E

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 116 (29 missing in structure)

  • Chain B: 3od8_M_N

    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: 451.30 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_E

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 12 32 E 0.4 1.2 %
    2 15 35 K 55.6 35.5 %
    3 16 36 S 29.5 74.6 %
    4 18 38 R 111.8 62.4 %
    5 19 39 A 24.4 100.0 %
    6 20 40 S 22.7 32.9 %
    7 22 42 K 21.8 19.2 %
    8 30 50 K 5.2 4.1 %
    9 34 54 R 19.1 100.0 %
    10 43 63 MSE 13.1 8.1 %
    11 44 64 F 70.4 69.7 %
    12 47 67 K 1.4 1.2 %
    13 48 68 V 29.0 80.4 %
    14 49 69 P 19.5 49.1 %
    15 51 71 W 27.4 90.2 %

  • Interface residues in 3od8_M_N

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 7 7:M1 T 2.2 1.1 %
    2 8 8:M1 G 82.7 43.2 %
    3 9 9:M1 G 103.5 65.3 %
    4 10 10:M1 G 146.3 52.0 %
    5 11 1:N1 C 49.8 23.3 %
    6 14 4:N1 A 4.4 2.6 %
    7 15 5:N1 A 38.2 22.3 %
    8 16 6:N1 G 18.9 10.6 %
    9 17 7:N1 C 5.2 3.1 %

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 9 9:M1 G 0.4
2 15 35 K 8 8:M1 G 47.7
3 15 35 K 9 9:M1 G 7.8
4 16 36 S 8 8:M1 G 13.3 H-bond
5 16 36 S 9 9:M1 G 15.9 H-bond
6 16 36 S 16 6:N1 G 0.2
7 18 38 R 7 7:M1 T 2.2
8 18 38 R 8 8:M1 G 21.7
9 18 38 R 9 9:M1 G 25.1
10 18 38 R 10 10:M1 G 1.6
11 18 38 R 14 4:N1 A 4.4
12 18 38 R 15 5:N1 A 38.2
13 18 38 R 16 6:N1 G 18.6
14 19 39 A 9 9:M1 G 18.1
15 19 39 A 10 10:M1 G 6.3
16 20 40 S 10 10:M1 G 22.7 H-bond
17 22 42 K 10 10:M1 G 21.8
18 30 50 K 17 7:N1 C 5.2
19 34 54 R 9 9:M1 G 19.1 H-bond
20 43 63 MSE 10 10:M1 G 11.5
21 43 63 MSE 11 1:N1 C 1.5
22 44 64 F 10 10:M1 G 22.1
23 44 64 F 11 1:N1 C 48.3
24 47 67 K 10 10:M1 G 1.4
25 48 68 V 10 10:M1 G 29.0
26 49 69 P 9 9:M1 G 2.6
27 49 69 P 10 10:M1 G 16.9
28 51 71 W 9 9:M1 G 14.4
29 51 71 W 10 10:M1 G 13.0

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_E; 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 = 40% (6/15), 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_E: 23 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 80

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


    Query: 147 LERARATTKKIEDLTELEGWEELEDNEK 174

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

    3od8_E: 81 GHSIRHPDVEVDGFSELR-WDDQQKVKK 107

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


    Download alignment FASTA file