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

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_A

    Title: POLY [ADP-RIBOSE] POLYMERASE 1

    Source organism: Homo sapiens

    Number of residues: 223 (137 missing in structure)

Buried interface area: 131.91 Å2

Number of inter-residue contacts at the interface: 10

  • Pairwise interaction

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  • Biological assembly

    Homomer, 4 proteins, 1 nucleic acid.

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Create a structural model for this interaction

Create a structural model for homo-oligomer

  • 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 %

  • 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 %

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

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% (0/5).

    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