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

PDB and SCOP data

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

Title: Human PARP-1 zinc finger 2 (Zn2) bound to DNA

Release date: 2011-01-12

Resolution: 2.8 Å

  • Chain A: 3odc_A

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 111 (18 missing in structure)

  • Chain B: 3odc_C_D

    Title: Nucleic acid

    Number of residues: 16

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

Buried interface area: 496.22 Å2

Number of inter-residue contacts at the interface: 31

Number of H-bonds: 7

  • Pairwise interaction

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    Download PyMOL visualization script

  • Biological assembly

    Homomer, 1 protein, 1 nucleic acid.

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Create a structural model for this interaction

  • Interface residues in 3odc_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 116 13 E <0.1 0.1 %
    2 119 16 K 57.0 36.0 %
    3 120 17 S 26.0 75.5 %
    4 121 18 N 22.4 34.1 %
    5 122 19 R 119.9 65.8 %
    6 123 20 S 28.2 98.7 %
    7 124 21 T 16.8 33.3 %
    8 126 23 K 27.3 42.9 %
    9 134 31 K 21.0 14.1 %
    10 138 35 R 19.3 100.0 %
    11 145 42 D 13.0 54.7 %
    12 148 45 K 28.9 27.9 %
    13 151 48 L 44.2 49.6 %
    14 154 51 I 35.4 74.9 %
    15 155 52 D 13.4 22.3 %
    16 156 53 R 1.0 2.4 %
    17 157 54 W 22.4 59.2 %

  • Interface residues in 3odc_C_D

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 4 4:C1 A <0.1 0.0 %
    2 5 5:C1 G 13.0 6.9 %
    3 6 6:C1 A 77.2 43.4 %
    4 7 7:C1 C 95.0 63.1 %
    5 8 8:C1 G 192.3 68.4 %
    6 9 1:D1 C 12.3 5.9 %
    7 12 4:D1 C 8.3 5.0 %
    8 13 5:D1 T 30.7 15.4 %
    9 14 6:D1 G 47.4 27.0 %
    10 15 7:D1 G 20.1 10.7 %

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
1 116 13 E 7 7:C1 C <0.1
2 119 16 K 6 6:C1 A 45.1 H-bond
3 119 16 K 7 7:C1 C 12.0
4 120 17 S 6 6:C1 A 12.2 H-bond
5 120 17 S 7 7:C1 C 12.1 H-bond
6 120 17 S 14 6:D1 G 1.7
7 121 18 N 14 6:D1 G 22.4
8 122 19 R 4 4:C1 A <0.1
9 122 19 R 5 5:C1 G 13.0
10 122 19 R 6 6:C1 A 19.9
11 122 19 R 7 7:C1 C 21.9
12 122 19 R 8 8:C1 G 3.8
13 122 19 R 12 4:D1 C 8.3
14 122 19 R 13 5:D1 T 30.7 H-bond
15 122 19 R 14 6:D1 G 22.4
16 123 20 S 7 7:C1 C 19.6
17 123 20 S 8 8:C1 G 8.7
18 124 21 T 8 8:C1 G 16.8 H-bond
19 126 23 K 8 8:C1 G 27.3
20 134 31 K 14 6:D1 G 0.9
21 134 31 K 15 7:D1 G 20.1 H-bond
22 138 35 R 7 7:C1 C 19.3 H-bond
23 145 42 D 8 8:C1 G 13.0
24 148 45 K 8 8:C1 G 28.9
25 151 48 L 8 8:C1 G 31.9
26 151 48 L 9 1:D1 C 12.3
27 154 51 I 8 8:C1 G 35.4
28 155 52 D 8 8:C1 G 13.4
29 156 53 R 8 8:C1 G 1.0
30 157 54 W 7 7:C1 C 10.1
31 157 54 W 8 8:C1 G 12.3

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: 3odc_A; Poly [ADP-ribose] polymerase 1

    Alignment data:

    Expectation value = 2.03e-4, Score = 45 bits (104),

    Identities = 28% (27/96), Positive = 47% (45/96), Gaps = 2% (2/96).

    Interface alignment data:

    Interface residues in alignment: 100% (17/17).

    Identities = 29% (5/17), Positive = 53% (9/17), Gaps = 0% (0/17).

    Query: 93 FCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLERARA 152

    F +YAK + CK C EKI KG R+ K + +P G + WYH C + R

    3odc_A: 10 FAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEKPQLGMIDRWYHPGCFVKN--REEL 67

    dssp: EEEEE------E------E-----EEEEEEEEE--EEEEEEEEEEE-HHHHHH- HHHH


    Query: 153 TTKKIEDLTELEGWEELEDNEKEQITQHIADLSSKA 188

    + ++L+G+ L +KE + + + + S+

    3odc_A: 68 GFRPEYSASQLKGFSLLATEDKEALKKQLPGVKSEG 103

    dssp: ------HHHHEE-HHH--HHHHHHHHHH---


    Download alignment FASTA file