Interaction between POLY [ADP-RIBOSE] POLYMERASE 1 (4av1_D) and Nucleic acid (4av1_X_Y)

PDB and SCOP data

PDB ID: 4av1 (all binary interactions in this PDB entry)

Title: Crystal structure of the human PARP-1 DNA binding domain in complex with DNA

Release date: 2012-06-13

Resolution: 3.1 Å

  • Chain A: 4av1_D

    Title: POLY [ADP-RIBOSE] POLYMERASE 1

    Source organism: Homo sapiens

    Number of residues: 223 (128 missing in structure)

  • Chain B: 4av1_X_Y

    Title: Nucleic acid

    Source organism: synthetic construct

    Number of residues: 24

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

Buried interface area: 554.28 Å2

Number of inter-residue contacts at the interface: 35

Number of H-bonds: 5

  • Pairwise interaction

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    Download PyMOL visualization script

  • Biological assembly

    Homomer, 4 proteins, 1 nucleic acid.

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Create a structural model for this interaction

  • Interface residues in 4av1_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 116 137 E 0.4 0.7 %
    2 118 139 A <0.1 0.7 %
    3 119 140 K 63.2 40.7 %
    4 120 141 S 25.4 79.9 %
    5 121 142 N 6.8 7.1 %
    6 122 143 R 107.8 65.7 %
    7 123 144 S 24.8 100.0 %
    8 124 145 T 19.9 49.0 %
    9 126 147 K 26.6 39.6 %
    10 134 155 K 10.3 7.2 %
    11 138 159 R 20.0 99.9 %
    12 145 166 D 16.7 80.5 %
    13 147 168 E 8.3 5.3 %
    14 148 169 K 41.3 35.2 %
    15 150 171 Q 7.4 5.4 %
    16 151 172 L 84.3 82.2 %
    17 152 173 G 0.1 0.9 %
    18 154 175 I 43.8 76.0 %
    19 155 176 D 22.6 41.4 %
    20 156 177 R 1.3 3.2 %
    21 157 178 W 23.4 67.7 %

  • Interface residues in 4av1_X_Y

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 9 9:X1 C 3.2 1.9 %
    2 10 10:X1 A 83.9 47.7 %
    3 11 11:X1 T 96.1 59.6 %
    4 12 12:X1 T 207.2 76.5 %
    5 13 1:Y1 T 60.1 21.4 %
    6 14 2:Y1 A 24.3 11.5 %
    7 15 3:Y1 A 3.7 2.0 %
    8 17 5:Y1 G 13.7 7.6 %
    9 18 6:Y1 C 27.1 14.9 %
    10 19 7:Y1 A 24.5 13.4 %
    11 20 8:Y1 A 10.3 5.7 %

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
1 116 137 E 11 11:X1 T 0.4
2 118 139 A 11 11:X1 T <0.1
3 119 140 K 10 10:X1 A 51.6
4 119 140 K 11 11:X1 T 11.6
5 120 141 S 10 10:X1 A 10.6 H-bond
6 120 141 S 11 11:X1 T 14.7 H-bond
7 121 142 N 19 7:Y1 A 6.8
8 122 143 R 9 9:X1 C 3.2
9 122 143 R 10 10:X1 A 21.7
10 122 143 R 11 11:X1 T 22.5
11 122 143 R 12 12:X1 T 1.8
12 122 143 R 17 5:Y1 G 13.7
13 122 143 R 18 6:Y1 C 27.1
14 122 143 R 19 7:Y1 A 17.7
15 123 144 S 11 11:X1 T 19.0
16 123 144 S 12 12:X1 T 5.8
17 124 145 T 12 12:X1 T 19.9 H-bond
18 126 147 K 12 12:X1 T 26.6
19 134 155 K 20 8:Y1 A 10.3
20 138 159 R 11 11:X1 T 20.0 H-bond
21 145 166 D 12 12:X1 T 16.7 H-bond
22 147 168 E 12 12:X1 T 8.3
23 148 169 K 12 12:X1 T 37.6
24 148 169 K 15 3:Y1 A 3.7
25 150 171 Q 13 1:Y1 T 7.4
26 151 172 L 12 12:X1 T 17.2
27 151 172 L 13 1:Y1 T 42.8
28 151 172 L 14 2:Y1 A 24.3
29 152 173 G 13 1:Y1 T 0.1
30 154 175 I 12 12:X1 T 34.0
31 154 175 I 13 1:Y1 T 9.8
32 155 176 D 12 12:X1 T 22.6
33 156 177 R 12 12:X1 T 1.3
34 157 178 W 11 11:X1 T 7.9
35 157 178 W 12 12:X1 T 15.5

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: 4av1_D; POLY [ADP-RIBOSE] POLYMERASE 1

    Alignment data:

    Expectation value = 7.89e-5, Score = 48 bits (113),

    Identities = 29% (29/100), Positive = 50% (50/100), Gaps = 6% (6/100).

    Interface alignment data:

    Interface residues in alignment: 0% (0/21).

    Identities = 0% (0/0), Positive = 0% (0/0), Gaps = 0% (0/0).

    Query: 89 AEQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLE 148

    +++ + V+YAK G A CKKC E I K R+ +V +P + G + WYH C ++

    4av1_D: 26 SDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKVGH 83

    dssp:


    Query: 149 RARATTKKIEDLTELEGWEELEDNEKEQITQHIADLSSKA 188

    R +++ +EL W +D +K + T ++ K

    4av1_D: 84 SIRHPDVEVDGFSELR-W---DDQQKVKKTAEAGGVTGKG 119

    dssp:


    Download alignment FASTA file