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

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_F

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 116 (26 missing in structure)

  • Chain B: 3oda_M_N

    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: 440.60 Å2

Number of inter-residue contacts at the interface: 26

Number of H-bonds: 3

  • Pairwise interaction

    Download PDB coordinates

    Download PyMOL visualization script

  • Biological assembly

    Homomer, 2 proteins, 1 nucleic acid.

    Download PDB coordinates


Create a structural model for this interaction

  • Interface residues in 3oda_F

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 15 35 K 56.3 37.2 %
    2 16 36 S 27.0 71.4 %
    3 18 38 R 90.3 44.9 %
    4 19 39 A 26.9 100.0 %
    5 20 40 S 16.9 30.1 %
    6 22 42 K 28.1 24.8 %
    7 34 54 R 19.2 99.0 %
    8 43 63 M 13.7 8.1 %
    9 44 64 F 69.0 75.1 %
    10 45 65 D 4.1 2.8 %
    11 47 67 K 5.4 8.7 %
    12 48 68 V 30.4 63.0 %
    13 49 69 P 27.3 57.7 %
    14 50 70 H 1.9 3.0 %
    15 51 71 W 24.2 74.5 %

  • Interface residues in 3oda_M_N

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 1 1:M1 G 76.6 34.5 %
    2 4 4:M1 T 6.7 3.6 %
    3 5 5:M1 G 18.7 10.8 %
    4 17 7:N1 A 5.1 3.0 %
    5 18 8:N1 G 92.9 47.1 %
    6 19 9:N1 G 100.8 63.9 %
    7 20 10:N1 C 139.8 52.7 %

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:N1 G 50.3
2 15 35 K 19 9:N1 G 6.1
3 16 36 S 18 8:N1 G 10.4
4 16 36 S 19 9:N1 G 16.6 H-bond
5 18 38 R 4 4:M1 T 6.7
6 18 38 R 5 5:M1 G 18.7
7 18 38 R 17 7:N1 A 5.1
8 18 38 R 18 8:N1 G 32.2
9 18 38 R 19 9:N1 G 26.1
10 18 38 R 20 10:N1 C 1.5
11 19 39 A 19 9:N1 G 19.0
12 19 39 A 20 10:N1 C 7.9
13 20 40 S 20 10:N1 C 16.9 H-bond
14 22 42 K 20 10:N1 C 28.1
15 34 54 R 19 9:N1 G 19.2 H-bond
16 43 63 M 1 1:M1 G 13.7
17 44 64 F 1 1:M1 G 58.8
18 44 64 F 20 10:N1 C 10.1
19 45 65 D 1 1:M1 G 4.1
20 47 67 K 20 10:N1 C 5.4
21 48 68 V 20 10:N1 C 30.4
22 49 69 P 19 9:N1 G 2.6
23 49 69 P 20 10:N1 C 24.7
24 50 70 H 20 10:N1 C 1.9
25 51 71 W 19 9:N1 G 11.4
26 51 71 W 20 10:N1 C 12.8

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_F; 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_F: 23 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 80

    dssp: ----EEEEE------E------E-----EEEEEEEE----- -EEEEEEEHHHHHH-


    Query: 147 LERARATTKKIEDLTELEGWEELEDNEK 174

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

    3oda_F: 81 GHSIRHPDVEVDGFSELR-WDDQQKVKK 107

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


    Download alignment FASTA file