Interaction between POLY [ADP-RIBOSE] POLYMERASE 1 (4av1_C) and POLY [ADP-RIBOSE] POLYMERASE 1 (4av1_D)

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_D

    Title: POLY [ADP-RIBOSE] POLYMERASE 1

    Source organism: Homo sapiens

    Number of residues: 223 (128 missing in structure)

Buried interface area: 151.27 Å2

Number of inter-residue contacts at the interface: 12

  • 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_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 41 62 S 2.5 22.6 %
    2 43 64 M 64.5 42.0 %
    3 44 65 F 55.1 43.2 %
    4 47 68 K 1.4 1.2 %
    5 48 69 V 25.5 49.1 %
    6 49 70 P 2.4 5.2 %

  • Interface residues in 4av1_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 144 165 V 32.8 54.3 %
    2 149 170 P 44.0 65.6 %
    3 150 171 Q 46.3 34.6 %
    4 152 173 G 4.4 31.4 %
    5 153 174 M 23.9 18.5 %

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 2.1
2 41 62 S 150 171 Q 0.3
3 43 64 M 144 165 V 30.8
4 43 64 M 149 170 P 5.5
5 43 64 M 152 173 G 4.4
6 43 64 M 153 174 M 23.9
7 44 65 F 144 165 V 2.0
8 44 65 F 149 170 P 36.3
9 44 65 F 150 171 Q 16.7
10 47 68 K 150 171 Q 1.4
11 48 69 V 150 171 Q 25.5
12 49 70 P 150 171 Q 2.4

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_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% (6/6).

    Identities = 0% (0/6), Positive = 33% (2/6), Gaps = 0% (0/6).

    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-


    Download alignment FASTA file