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

PDB and SCOP data

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

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

Release date: 2011-01-12

Resolution: 3.0 Å

  • Chain A: 3ode_A

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 111 (20 missing in structure)

  • Chain B: 3ode_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: 521.01 Å2

Number of inter-residue contacts at the interface: 34

Number of H-bonds: 5

  • 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 3ode_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 116 13 E <0.1 0.0 %
    2 118 15 A 0.3 8.4 %
    3 119 16 K 61.8 37.7 %
    4 120 17 S 32.4 90.1 %
    5 121 18 N 20.5 33.7 %
    6 122 19 R 128.4 72.1 %
    7 123 20 S 26.6 100.0 %
    8 124 21 T 15.8 33.9 %
    9 126 23 K 29.4 38.5 %
    10 134 31 K 26.1 17.7 %
    11 138 35 R 19.6 99.8 %
    12 145 42 D 10.0 36.1 %
    13 148 45 K 22.5 24.1 %
    14 151 48 L 51.9 56.7 %
    15 154 51 I 36.7 71.8 %
    16 155 52 D 16.5 38.4 %
    17 156 53 R <0.1 0.1 %
    18 157 54 W 22.3 65.0 %

  • Interface residues in 3ode_C_D

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 5 5:C1 A 13.0 7.2 %
    2 6 6:C1 G 82.1 45.1 %
    3 7 7:C1 C 94.6 63.4 %
    4 8 8:C1 G 184.7 65.9 %
    5 9 1:D1 C 22.1 10.7 %
    6 12 4:D1 T 11.1 6.1 %
    7 13 5:D1 T 30.9 15.9 %
    8 14 6:D1 G 54.0 30.1 %
    9 15 7:D1 G 28.6 15.0 %

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
1 116 13 E 7 7:C1 C <0.1
2 118 15 A 7 7:C1 C 0.3
3 119 16 K 6 6:C1 G 47.3
4 119 16 K 7 7:C1 C 12.7
5 119 16 K 15 7:D1 G 1.8
6 120 17 S 6 6:C1 G 13.8 H-bond
7 120 17 S 7 7:C1 C 12.0 H-bond
8 120 17 S 14 6:D1 G 5.6
9 120 17 S 15 7:D1 G 1.1
10 121 18 N 14 6:D1 G 20.5
11 122 19 R 5 5:C1 A 13.0
12 122 19 R 6 6:C1 G 21.0
13 122 19 R 7 7:C1 C 20.8
14 122 19 R 8 8:C1 G 4.1
15 122 19 R 12 4:D1 T 11.1 H-bond
16 122 19 R 13 5:D1 T 30.9
17 122 19 R 14 6:D1 G 27.4
18 123 20 S 7 7:C1 C 18.6
19 123 20 S 8 8:C1 G 7.9
20 124 21 T 8 8:C1 G 15.8 H-bond
21 126 23 K 8 8:C1 G 29.4
22 134 31 K 14 6:D1 G 0.4
23 134 31 K 15 7:D1 G 25.7
24 138 35 R 7 7:C1 C 19.6 H-bond
25 145 42 D 8 8:C1 G 10.0
26 148 45 K 8 8:C1 G 22.5
27 151 48 L 8 8:C1 G 29.8
28 151 48 L 9 1:D1 C 22.1
29 154 51 I 8 8:C1 G 36.7
30 155 52 D 7 7:C1 C <0.1
31 155 52 D 8 8:C1 G 16.5
32 156 53 R 8 8:C1 G <0.1
33 157 54 W 7 7:C1 C 10.4
34 157 54 W 8 8:C1 G 11.8

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: 3ode_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% (18/18).

    Identities = 33% (6/18), Positive = 56% (10/18), Gaps = 0% (0/18).

    Query: 93 FCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLERARA 152

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

    3ode_A: 10 FAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEKPQLGMIDRWYHPGCFVKN--REEL 67

    dssp: EEEEE------E------E-----EEEEEEEE----HHH-EEEEEE-HHHHHH- ----


    Query: 153 TTKKIEDLTELEGWEELEDNEKEQITQHIADLSSKA 188

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

    3ode_A: 68 GFRPEYSASQLKGFSLLATEDKEALKKQLPGVKSEG 103

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


    Download alignment FASTA file