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

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_B

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 111 (18 missing in structure)

  • Chain B: 3ode_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: 529.02 Å2

Number of inter-residue contacts at the interface: 35

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 3ode_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 118 15 A <0.1 0.9 %
    2 119 16 K 58.5 37.6 %
    3 120 17 S 30.4 90.6 %
    4 121 18 N 26.9 36.6 %
    5 122 19 R 123.9 78.4 %
    6 123 20 S 26.9 100.0 %
    7 124 21 T 14.5 37.6 %
    8 126 23 K 31.3 39.0 %
    9 134 31 K 29.5 20.0 %
    10 138 35 R 20.5 99.5 %
    11 148 45 K 24.3 24.8 %
    12 150 47 Q 26.8 20.0 %
    13 151 48 L 51.9 56.5 %
    14 154 51 I 34.7 54.5 %
    15 155 52 D 9.1 18.9 %
    16 156 53 R <0.1 0.0 %
    17 157 54 W 19.9 65.5 %

  • Interface residues in 3ode_E_F

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 5 5:E1 A 13.8 7.8 %
    2 6 6:E1 G 78.0 41.7 %
    3 7 7:E1 C 91.3 61.1 %
    4 8 8:E1 G 152.1 52.1 %
    5 9 1:F1 C 64.1 31.4 %
    6 10 2:F1 G 1.8 0.9 %
    7 12 4:F1 T 10.2 5.7 %
    8 13 5:F1 T 29.9 16.0 %
    9 14 6:F1 G 57.0 33.3 %
    10 15 7:F1 G 30.8 16.8 %

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
1 118 15 A 7 7:E1 C <0.1
2 119 16 K 6 6:E1 G 43.5
3 119 16 K 7 7:E1 C 14.1
4 119 16 K 15 7:F1 G 0.9
5 120 17 S 6 6:E1 G 12.2 H-bond
6 120 17 S 7 7:E1 C 12.2 H-bond
7 120 17 S 14 6:F1 G 5.7
8 120 17 S 15 7:F1 G 0.3
9 121 18 N 14 6:F1 G 25.7
10 121 18 N 15 7:F1 G 1.2
11 122 19 R 5 5:E1 A 13.8
12 122 19 R 6 6:E1 G 22.3
13 122 19 R 7 7:E1 C 20.3
14 122 19 R 8 8:E1 G 2.7
15 122 19 R 12 4:F1 T 10.2 H-bond
16 122 19 R 13 5:F1 T 29.9 H-bond
17 122 19 R 14 6:F1 G 24.6
18 123 20 S 7 7:E1 C 17.6
19 123 20 S 8 8:E1 G 9.3
20 124 21 T 8 8:E1 G 14.5 H-bond
21 126 23 K 8 8:E1 G 31.3
22 134 31 K 14 6:F1 G 1.0
23 134 31 K 15 7:F1 G 28.4 H-bond
24 138 35 R 7 7:E1 C 20.5 H-bond
25 148 45 K 8 8:E1 G 13.2
26 148 45 K 9 1:F1 C 9.3
27 148 45 K 10 2:F1 G 1.8
28 150 47 Q 9 1:F1 C 26.8
29 151 48 L 8 8:E1 G 23.9
30 151 48 L 9 1:F1 C 28.0
31 154 51 I 8 8:E1 G 34.7
32 155 52 D 8 8:E1 G 9.1
33 156 53 R 8 8:E1 G <0.1
34 157 54 W 7 7:E1 C 6.5
35 157 54 W 8 8:E1 G 13.4

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_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% (17/17).

    Identities = 35% (6/17), Positive = 47% (8/17), Gaps = 0% (0/17).

    Query: 93 FCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLERARA 152

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

    3ode_B: 10 FAAEYAKSNRSTCKGCMEKIEKGQVRLSKKMVDPEKPQLGMIDRWYHPGCFVKN--REEL 67

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


    Query: 153 TTKKIEDLTELEGWEELEDNEKEQITQHIADLSSKA 188

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

    3ode_B: 68 GFRPEYSASQLKGFSLLATEDKEALKKQLPGVKSEG 103

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


    Download alignment FASTA file