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

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_B

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 111 (11 missing in structure)

  • Chain B: 3odc_E_F

    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: 482.44 Å2

Number of inter-residue contacts at the interface: 33

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 3odc_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 116 13 E 0.1 0.3 %
    2 118 15 A <0.1 0.1 %
    3 119 16 K 47.2 29.3 %
    4 120 17 S 28.7 79.3 %
    5 121 18 N 16.7 20.4 %
    6 122 19 R 113.1 70.1 %
    7 123 20 S 25.5 100.0 %
    8 124 21 T 14.2 50.7 %
    9 126 23 K 26.5 31.0 %
    10 134 31 K 22.7 15.7 %
    11 138 35 R 19.7 99.8 %
    12 148 45 K 22.2 24.1 %
    13 150 47 Q 30.1 22.1 %
    14 151 48 L 47.1 55.6 %
    15 154 51 I 34.7 59.0 %
    16 155 52 D 10.5 22.5 %
    17 156 53 R <0.1 0.0 %
    18 157 54 W 23.3 69.3 %

  • Interface residues in 3odc_E_F

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 5 5:E1 G 12.8 7.5 %
    2 6 6:E1 A 69.9 38.6 %
    3 7 7:E1 C 92.0 60.9 %
    4 8 8:E1 G 151.4 52.1 %
    5 9 1:F1 C 59.2 29.4 %
    6 10 2:F1 G 0.7 0.4 %
    7 12 4:F1 C 8.2 4.8 %
    8 13 5:F1 T 28.3 14.4 %
    9 14 6:F1 G 40.6 23.0 %
    10 15 7:F1 G 19.3 10.6 %

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
1 116 13 E 7 7:E1 C 0.1
2 118 15 A 7 7:E1 C <0.1
3 119 16 K 6 6:E1 A 36.8
4 119 16 K 7 7:E1 C 10.3
5 120 17 S 6 6:E1 A 13.2 H-bond
6 120 17 S 7 7:E1 C 14.7 H-bond
7 120 17 S 14 6:F1 G 0.8
8 121 18 N 14 6:F1 G 16.7
9 122 19 R 5 5:E1 G 12.8
10 122 19 R 6 6:E1 A 19.9
11 122 19 R 7 7:E1 C 21.5
12 122 19 R 8 8:E1 G 2.8
13 122 19 R 12 4:F1 C 8.2 H-bond
14 122 19 R 13 5:F1 T 28.3
15 122 19 R 14 6:F1 G 19.7
16 123 20 S 7 7:E1 C 17.4
17 123 20 S 8 8:E1 G 8.0
18 124 21 T 8 8:E1 G 14.2 H-bond
19 126 23 K 8 8:E1 G 26.5
20 134 31 K 14 6:F1 G 3.4
21 134 31 K 15 7:F1 G 19.3
22 138 35 R 7 7:E1 C 19.7 H-bond
23 148 45 K 8 8:E1 G 16.6
24 148 45 K 9 1:F1 C 4.9
25 148 45 K 10 2:F1 G 0.7
26 150 47 Q 9 1:F1 C 30.1
27 151 48 L 8 8:E1 G 23.0
28 151 48 L 9 1:F1 C 24.2
29 154 51 I 8 8:E1 G 34.7
30 155 52 D 8 8:E1 G 10.5
31 156 53 R 8 8:E1 G <0.1
32 157 54 W 7 7:E1 C 8.3
33 157 54 W 8 8:E1 G 15.1

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_B; 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 = 50% (9/18), Gaps = 0% (0/18).

    Query: 93 FCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLERARA 152

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

    3odc_B: 10 FAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEKPQLGMIDRWYHPGCFVKN--REEL 67

    dssp: EEEEE------E------E-----EEEEEEE-----HHH--EEEEE-HHHHHH- ----


    Query: 153 TTKKIEDLTELEGWEELEDNEKEQITQHIADLSSKA 188

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

    3odc_B: 68 GFRPEYSASQLKGFSLLATEDKEALKKQLPGVKSEG 103

    dssp: -------HHH-E-HHH--HHHHHHHHHH-----


    Download alignment FASTA file