Interaction between POLY [ADP-RIBOSE] POLYMERASE 1 (4av1_A) and POLY [ADP-RIBOSE] POLYMERASE 1 (4av1_B)

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_B

    Title: POLY [ADP-RIBOSE] POLYMERASE 1

    Source organism: Homo sapiens

    Number of residues: 223 (127 missing in structure)

Buried interface area: 131.91 Å2

Number of inter-residue contacts at the interface: 10

  • 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

Create a structural model for homo-oligomer

  • Interface residues in 4av1_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 41 62 S 1.1 14.6 %
    2 43 64 M 60.5 40.1 %
    3 44 65 F 49.0 40.2 %
    4 48 69 V 21.3 40.2 %

  • Interface residues in 4av1_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 144 165 V 27.2 44.5 %
    2 149 170 P 46.9 72.2 %
    3 150 171 Q 44.2 32.9 %
    4 152 173 G 12.0 49.0 %
    5 153 174 M 1.5 1.1 %

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. in chain B sequence Residue in chain B Contact area, Å2 Contact type
1 41 62 S 149 170 P <0.1
2 41 62 S 150 171 Q 1.0
3 43 64 M 144 165 V 27.2
4 43 64 M 149 170 P 19.6
5 43 64 M 150 171 Q 0.2
6 43 64 M 152 173 G 12.0
7 43 64 M 153 174 M 1.5
8 44 65 F 149 170 P 27.3
9 44 65 F 150 171 Q 21.7
10 48 69 V 150 171 Q 21.3

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% (4/4).

    Identities = 0% (0/4), Positive = 50% (2/4), Gaps = 0% (0/4).

    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