Interaction between Poly [ADP-ribose] polymerase 1 (3oda_B) and Nucleic acid (3oda_I_J)

PDB and SCOP data

PDB ID: 3oda (all binary interactions in this PDB entry)

Title: Human PARP-1 zinc finger 1 (Zn1) bound to DNA

Release date: 2011-01-12

Resolution: 2.6 Å

  • Chain A: 3oda_B

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 116 (30 missing in structure)

  • Chain B: 3oda_I_J

    Title: Nucleic acid

    Number of residues: 20

    Note: Residues of nucleic acid domain are renumbered to avoid repeating the same residue numbers from different PDB chains.

Buried interface area: 441.80 Å2

Number of inter-residue contacts at the interface: 26

Number of H-bonds: 4

  • Pairwise interaction

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    Download PyMOL visualization script

  • Biological assembly

    Homomer, 2 proteins, 1 nucleic acid.

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Create a structural model for this interaction

  • Interface residues in 3oda_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 15 35 K 51.3 33.7 %
    2 16 36 S 28.7 73.0 %
    3 18 38 R 98.4 50.4 %
    4 19 39 A 27.5 100.0 %
    5 20 40 S 16.8 30.4 %
    6 22 42 K 27.8 24.5 %
    7 34 54 R 19.6 99.1 %
    8 43 63 M 11.6 7.3 %
    9 44 64 F 68.7 67.6 %
    10 45 65 D <0.1 0.1 %
    11 47 67 K 5.7 7.1 %
    12 48 68 V 31.9 64.4 %
    13 49 69 P 27.0 58.6 %
    14 50 70 H 2.8 4.5 %
    15 51 71 W 23.9 73.2 %

  • Interface residues in 3oda_I_J

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 1 1:I1 G 70.5 30.2 %
    2 4 4:I1 T 6.0 3.3 %
    3 5 5:I1 G 24.6 13.9 %
    4 17 7:J1 A 9.0 5.1 %
    5 18 8:J1 G 88.8 44.1 %
    6 19 9:J1 G 99.6 65.4 %
    7 20 10:J1 C 143.5 53.5 %

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. of chain B in PDB Residue in chain B Contact area, Å2 Contact type
1 15 35 K 18 8:J1 G 44.2
2 15 35 K 19 9:J1 G 7.1
3 16 36 S 18 8:J1 G 12.6 H-bond
4 16 36 S 19 9:J1 G 16.1 H-bond
5 18 38 R 4 4:I1 T 6.0
6 18 38 R 5 5:I1 G 24.6
7 18 38 R 17 7:J1 A 9.0
8 18 38 R 18 8:J1 G 32.0
9 18 38 R 19 9:J1 G 25.0
10 18 38 R 20 10:J1 C 1.9
11 19 39 A 19 9:J1 G 19.6
12 19 39 A 20 10:J1 C 8.0
13 20 40 S 20 10:J1 C 16.8 H-bond
14 22 42 K 20 10:J1 C 27.8
15 34 54 R 19 9:J1 G 19.6 H-bond
16 43 63 M 1 1:I1 G 11.6
17 44 64 F 1 1:I1 G 58.8
18 44 64 F 20 10:J1 C 10.0
19 45 65 D 1 1:I1 G <0.1
20 47 67 K 20 10:J1 C 5.7
21 48 68 V 20 10:J1 C 31.9
22 49 69 P 19 9:J1 G 1.2
23 49 69 P 20 10:J1 C 25.8
24 50 70 H 20 10:J1 C 2.8
25 51 71 W 19 9:J1 G 11.0
26 51 71 W 20 10:J1 C 12.9

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: 3oda_B; Poly [ADP-ribose] polymerase 1

    Alignment data:

    Expectation value = 3.15e-6, Score = 50 bits (118),

    Identities = 31% (27/88), Positive = 53% (47/88), Gaps = 3% (3/88).

    Interface alignment data:

    Interface residues in alignment: 100% (15/15).

    Identities = 33% (5/15), Positive = 47% (7/15), Gaps = 0% (0/15).

    Query: 87 EMAEQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEK 146

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

    3oda_B: 23 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 80

    dssp: ---EEEEE------E------E-----EEEEEEEE----- -EEEEEEEHHHHH--


    Query: 147 LERARATTKKIEDLTELEGWEELEDNEK 174

    R +++ +EL W++ + +K

    3oda_B: 81 GHSIRHPDVEVDGFSELR-WDDQQKVKK 107

    dssp: ------HHHHEE-HHH-- HHHHHHHHH


    Download alignment FASTA file