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

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_C

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 116 (29 missing in structure)

  • Chain B: 3oda_K_L

    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: 486.79 Å2

Number of inter-residue contacts at the interface: 30

Number of H-bonds: 3

  • 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_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 12 32 E 0.4 2.2 %
    2 15 35 K 58.4 37.8 %
    3 16 36 S 26.1 70.1 %
    4 18 38 R 113.7 57.9 %
    5 19 39 A 25.5 100.0 %
    6 20 40 S 20.7 31.8 %
    7 22 42 K 24.4 21.9 %
    8 34 54 R 19.8 100.0 %
    9 41 61 S <0.1 0.1 %
    10 43 63 M 56.7 32.8 %
    11 44 64 F 66.5 68.6 %
    12 45 65 D 1.6 1.2 %
    13 47 67 K <0.1 0.1 %
    14 48 68 V 28.3 77.0 %
    15 49 69 P 19.1 38.6 %
    16 50 70 H <0.1 0.1 %
    17 51 71 W 25.6 79.0 %

  • Interface residues in 3oda_K_L

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 7 7:K1 A 4.2 2.5 %
    2 8 8:K1 G 90.6 46.5 %
    3 9 9:K1 G 103.9 65.2 %
    4 10 10:K1 C 156.7 59.6 %
    5 11 1:L1 G 79.8 34.0 %
    6 14 4:L1 T 2.7 1.3 %
    7 15 5:L1 G 37.6 22.6 %
    8 16 6:L1 C 11.2 6.6 %

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 12 32 E 9 9:K1 G 0.4
2 15 35 K 8 8:K1 G 49.9
3 15 35 K 9 9:K1 G 8.5
4 16 36 S 8 8:K1 G 10.6
5 16 36 S 9 9:K1 G 15.5 H-bond
6 18 38 R 7 7:K1 A 4.2
7 18 38 R 8 8:K1 G 30.1
8 18 38 R 9 9:K1 G 26.6
9 18 38 R 10 10:K1 C 1.2
10 18 38 R 14 4:L1 T 2.7
11 18 38 R 15 5:L1 G 37.6
12 18 38 R 16 6:L1 C 11.2
13 19 39 A 9 9:K1 G 18.9
14 19 39 A 10 10:K1 C 6.6
15 20 40 S 10 10:K1 C 20.7 H-bond
16 22 42 K 10 10:K1 C 24.4
17 34 54 R 9 9:K1 G 19.8 H-bond
18 41 61 S 10 10:K1 C <0.1
19 43 63 M 10 10:K1 C 35.4
20 43 63 M 11 1:L1 G 21.3
21 44 64 F 10 10:K1 C 9.5
22 44 64 F 11 1:L1 G 56.9
23 45 65 D 11 1:L1 G 1.6
24 47 67 K 10 10:K1 C <0.1
25 48 68 V 10 10:K1 C 28.3
26 49 69 P 9 9:K1 G 1.6
27 49 69 P 10 10:K1 C 17.5
28 50 70 H 10 10:K1 C <0.1
29 51 71 W 9 9:K1 G 12.7
30 51 71 W 10 10:K1 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_C; 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% (17/17).

    Identities = 29% (5/17), Positive = 53% (9/17), Gaps = 0% (0/17).

    Query: 87 EMAEQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEK 146

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

    3oda_C: 23 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 80

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


    Query: 147 LERARATTKKIEDLTELEGWEELEDNEK 174

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

    3oda_C: 81 GHSIRHPDVEVDGFSELR-WDDQQKVKK 107

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


    Download alignment FASTA file