Interaction between POLY [ADP-RIBOSE] POLYMERASE 1 (4av1_A) 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_A

    Title: POLY [ADP-RIBOSE] POLYMERASE 1

    Source organism: Homo sapiens

    Number of residues: 223 (137 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: 339.44 Å2

Number of inter-residue contacts at the interface: 25

Number of H-bonds: 5

  • Pairwise interaction

    Download PDB coordinates

    Download PyMOL visualization script

  • Biological assembly

    Homomer, 4 proteins, 1 nucleic acid.

    Download PDB coordinates


Create a structural model for this interaction

  • Interface residues in 4av1_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 15 36 K 52.7 30.1 %
    2 16 37 S 42.4 90.1 %
    3 18 39 R 115.0 59.3 %
    4 19 40 A 18.9 93.1 %
    5 20 41 S 22.1 37.8 %
    6 22 43 K 26.2 25.1 %
    7 30 51 K 2.4 1.7 %
    8 34 55 R 19.2 93.6 %
    9 48 69 V 2.0 3.6 %
    10 49 70 P 8.1 14.5 %
    11 50 71 H <0.1 0.0 %
    12 51 72 W 30.4 69.3 %

  • 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 16.7 5.9 %
    2 2 2:X1 A 125.0 62.1 %
    3 3 3:X1 G 100.5 56.8 %
    4 4 4:X1 T 60.9 33.2 %
    5 5 5:X1 G 0.1 0.1 %
    6 21 9:Y1 C 15.8 8.8 %
    7 22 10:Y1 A 13.4 7.3 %
    8 23 11:Y1 C 7.0 4.4 %

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 3 3:X1 G 21.9
2 15 36 K 4 4:X1 T 30.8 H-bond
3 16 37 S 3 3:X1 G 29.6
4 16 37 S 4 4:X1 T 12.8
5 18 39 R 2 2:X1 A 41.3
6 18 39 R 3 3:X1 G 22.4 H-bond
7 18 39 R 4 4:X1 T 14.9
8 18 39 R 5 5:X1 G 0.1
9 18 39 R 21 9:Y1 C 15.8
10 18 39 R 22 10:Y1 A 13.4
11 18 39 R 23 11:Y1 C 7.0
12 19 40 A 2 2:X1 A 14.9
13 19 40 A 3 3:X1 G 4.1
14 20 41 S 2 2:X1 A 22.1 H-bond
15 22 43 K 1 1:X1 A 12.7
16 22 43 K 2 2:X1 A 13.5 H-bond
17 30 51 K 4 4:X1 T 2.4
18 34 55 R 2 2:X1 A 1.2
19 34 55 R 3 3:X1 G 18.1 H-bond
20 48 69 V 1 1:X1 A 2.0
21 49 70 P 1 1:X1 A 1.9
22 49 70 P 2 2:X1 A 6.1
23 50 71 H 2 2:X1 A <0.1
24 51 72 W 2 2:X1 A 26.0
25 51 72 W 3 3:X1 G 4.4

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: 4av1_A; 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% (12/12).

    Identities = 50% (6/12), Positive = 58% (7/12), Gaps = 0% (0/12).

    Query: 89 AEQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLE 148

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

    4av1_A: 26 SDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKVGH 83

    dssp: ---EEEEE------E------E-----EEEEEEEEE---- EEEEEEEEHHHH-----


    Query: 149 RARATTKKIEDLTELEGWEELEDNEKEQITQHIADLSSKA 188

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

    4av1_A: 84 SIRHPDVEVDGFSELR-W---DDQQKVKKTAEAGGVTGKG 119

    dssp: ----HHHHEE------ H HHHHHHHHHHH-


    Download alignment FASTA file