Interaction between POLY [ADP-RIBOSE] POLYMERASE 1 (4av1_B) 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_B

    Title: POLY [ADP-RIBOSE] POLYMERASE 1

    Source organism: Homo sapiens

    Number of residues: 223 (127 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: 551.01 Å2

Number of inter-residue contacts at the interface: 34

Number of H-bonds: 4

  • 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_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 118 139 A 0.1 4.0 %
    2 119 140 K 59.8 38.3 %
    3 120 141 S 24.5 78.6 %
    4 121 142 N 4.2 4.3 %
    5 122 143 R 111.5 68.0 %
    6 123 144 S 23.8 100.0 %
    7 124 145 T 19.6 47.7 %
    8 126 147 K 23.8 36.2 %
    9 134 155 K 10.5 7.3 %
    10 138 159 R 20.3 98.9 %
    11 145 166 D 13.8 66.2 %
    12 147 168 E 0.3 0.2 %
    13 148 169 K 46.4 40.9 %
    14 150 171 Q 13.2 9.8 %
    15 151 172 L 77.9 85.2 %
    16 153 174 M 7.0 5.2 %
    17 154 175 I 44.6 80.0 %
    18 155 176 D 24.8 44.0 %
    19 156 177 R 1.3 3.2 %
    20 157 178 W 23.7 68.6 %

  • Interface residues in 4av1_X_Y

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 1 1:X1 A 66.9 24.5 %
    2 2 2:X1 A 24.7 11.2 %
    3 3 3:X1 G 12.5 6.7 %
    4 5 5:X1 G 11.4 6.5 %
    5 6 6:X1 T 31.4 16.5 %
    6 7 7:X1 T 21.3 11.1 %
    7 8 8:X1 G 10.5 5.4 %
    8 21 9:Y1 C 4.9 2.7 %
    9 22 10:Y1 A 84.1 45.9 %
    10 23 11:Y1 C 91.3 67.0 %
    11 24 12:Y1 T 192.2 71.1 %

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
1 118 139 A 23 11:Y1 C 0.1
2 119 140 K 22 10:Y1 A 49.8
3 119 140 K 23 11:Y1 C 10.1
4 120 141 S 22 10:Y1 A 10.8 H-bond
5 120 141 S 23 11:Y1 C 13.6 H-bond
6 121 142 N 7 7:X1 T 4.2
7 122 143 R 5 5:X1 G 11.4
8 122 143 R 6 6:X1 T 31.4
9 122 143 R 7 7:X1 T 17.1
10 122 143 R 21 9:Y1 C 4.9
11 122 143 R 22 10:Y1 A 23.5
12 122 143 R 23 11:Y1 C 21.6
13 122 143 R 24 12:Y1 T 1.7
14 123 144 S 23 11:Y1 C 17.4
15 123 144 S 24 12:Y1 T 6.4
16 124 145 T 24 12:Y1 T 19.6 H-bond
17 126 147 K 24 12:Y1 T 23.8
18 134 155 K 8 8:X1 G 10.5
19 138 159 R 23 11:Y1 C 20.3 H-bond
20 145 166 D 24 12:Y1 T 13.8
21 147 168 E 24 12:Y1 T 0.3
22 148 169 K 3 3:X1 G 12.5
23 148 169 K 24 12:Y1 T 33.9
24 150 171 Q 1 1:X1 A 13.2
25 151 172 L 1 1:X1 A 35.6
26 151 172 L 2 2:X1 A 24.7
27 151 172 L 24 12:Y1 T 17.6
28 153 174 M 1 1:X1 A 7.0
29 154 175 I 1 1:X1 A 11.0
30 154 175 I 24 12:Y1 T 33.7
31 155 176 D 24 12:Y1 T 24.8
32 156 177 R 24 12:Y1 T 1.3
33 157 178 W 23 11:Y1 C 8.2
34 157 178 W 24 12:Y1 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_B; 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% (0/20).

    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_B: 26 SDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKVGH 83

    dssp:


    Query: 149 RARATTKKIEDLTELEGWEELEDNEKEQITQHIADLSSKA 188

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

    4av1_B: 84 SIRHPDVEVDGFSELR-W---DDQQKVKKTAEAGGVTGKG 119

    dssp:


    Download alignment FASTA file