Interaction between POLY [ADP-RIBOSE] POLYMERASE 1 (4av1_C) 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_C

    Title: POLY [ADP-RIBOSE] POLYMERASE 1

    Source organism: Homo sapiens

    Number of residues: 223 (138 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: 327.17 Å2

Number of inter-residue contacts at the interface: 24

Number of H-bonds: 2

  • Pairwise interaction

  • Biological assembly

    Homomer, 4 proteins, 1 nucleic acid.


  • Interface residues in 4av1_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 15 36 K 47.7 29.8 %
    2 16 37 S 41.8 86.1 %
    3 18 39 R 109.7 55.9 %
    4 19 40 A 18.9 92.9 %
    5 20 41 S 23.6 41.0 %
    6 22 43 K 26.5 25.4 %
    7 34 55 R 18.4 99.4 %
    8 48 69 V 2.7 4.8 %
    9 49 70 P 8.6 18.2 %
    10 50 71 H <0.1 0.0 %
    11 51 72 W 29.3 78.3 %

  • 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 17.3 10.2 %
    2 10 10:X1 A 13.8 7.9 %
    3 11 11:X1 T 3.6 1.9 %
    4 13 1:Y1 T 22.6 7.9 %
    5 14 2:Y1 A 121.1 63.4 %
    6 15 3:Y1 A 102.9 59.7 %
    7 16 4:Y1 T 45.9 23.8 %

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 15 36 K 15 3:Y1 A 30.5
2 15 36 K 16 4:Y1 T 17.1
3 16 37 S 15 3:Y1 A 29.0
4 16 37 S 16 4:Y1 T 12.8
5 18 39 R 9 9:X1 C 17.3
6 18 39 R 10 10:X1 A 13.8
7 18 39 R 11 11:X1 T 3.6
8 18 39 R 14 2:Y1 A 38.6
9 18 39 R 15 3:Y1 A 20.6
10 18 39 R 16 4:Y1 T 15.9
11 19 40 A 14 2:Y1 A 14.9
12 19 40 A 15 3:Y1 A 3.9
13 20 41 S 13 1:Y1 T 3.8
14 20 41 S 14 2:Y1 A 19.8 H-bond
15 22 43 K 13 1:Y1 T 13.9
16 22 43 K 14 2:Y1 A 12.6
17 34 55 R 14 2:Y1 A 2.2
18 34 55 R 15 3:Y1 A 16.2 H-bond
19 48 69 V 13 1:Y1 T 2.7
20 49 70 P 13 1:Y1 T 2.2
21 49 70 P 14 2:Y1 A 6.4
22 50 71 H 14 2:Y1 A <0.1
23 51 72 W 14 2:Y1 A 26.6
24 51 72 W 15 3:Y1 A 2.7

  • Query protein: sp|P49916|DNLI3_HUMAN DNA ligase 3 OS=Homo sapiens GN=LIG3 PE=1 SV=2

    Result domain: 4av1_C; 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: 100% (11/11).

    Identities = 45% (5/11), Positive = 55% (6/11), Gaps = 0% (0/11).

    Query: 89 AEQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLE 148

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

    4av1_C: 26 SDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKVGH 83

    dssp: ---EEEEE------E------E-----EEEEEEEE----- -EEEEEEEHHHHHHH--


    Query: 149 RARATTKKIEDLTELEGWEELEDNEKEQITQHIADLSSKA 188

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

    4av1_C: 84 SIRHPDVEVDGFSELR-W---DDQQKVKKTAEAGGVTGKG 119

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