Interaction between Poly [ADP-ribose] polymerase 1 (3oda_D) 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_D

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 116 (27 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: 444.95 Å2

Number of inter-residue contacts at the interface: 27

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_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 12 32 E <0.1 0.1 %
    2 15 35 K 55.3 36.2 %
    3 16 36 S 26.7 70.9 %
    4 18 38 R 87.3 43.1 %
    5 19 39 A 26.9 100.0 %
    6 20 40 S 16.2 29.6 %
    7 22 42 K 28.0 25.0 %
    8 34 54 R 19.9 99.7 %
    9 43 63 M 17.1 11.1 %
    10 44 64 F 73.1 77.7 %
    11 45 65 D 3.6 2.4 %
    12 47 67 K 5.2 8.5 %
    13 48 68 V 30.4 65.9 %
    14 49 69 P 28.0 59.1 %
    15 50 70 H 2.6 4.2 %
    16 51 71 W 24.7 77.8 %

  • Interface residues in 3oda_K_L

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 1 1:K1 G 82.1 36.0 %
    2 4 4:K1 T 6.5 3.5 %
    3 5 5:K1 G 14.9 8.4 %
    4 17 7:L1 A 7.1 4.2 %
    5 18 8:L1 G 89.9 45.9 %
    6 19 9:L1 G 102.8 64.4 %
    7 20 10:L1 C 141.5 53.2 %

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. of chain B in PDB Residue in chain B Contact area, Å2 Contact type
1 12 32 E 19 9:L1 G <0.1
2 15 35 K 18 8:L1 G 48.7
3 15 35 K 19 9:L1 G 6.6
4 16 36 S 18 8:L1 G 11.2
5 16 36 S 19 9:L1 G 15.5 H-bond
6 18 38 R 4 4:K1 T 6.5
7 18 38 R 5 5:K1 G 14.9
8 18 38 R 17 7:L1 A 7.1
9 18 38 R 18 8:L1 G 30.0
10 18 38 R 19 9:L1 G 26.3
11 18 38 R 20 10:L1 C 2.3
12 19 39 A 19 9:L1 G 18.3
13 19 39 A 20 10:L1 C 8.6
14 20 40 S 20 10:L1 C 16.2 H-bond
15 22 42 K 20 10:L1 C 28.0
16 34 54 R 19 9:L1 G 19.9 H-bond
17 43 63 M 1 1:K1 G 17.1
18 44 64 F 1 1:K1 G 61.4
19 44 64 F 20 10:L1 C 11.8
20 45 65 D 1 1:K1 G 3.6
21 47 67 K 20 10:L1 C 5.2
22 48 68 V 20 10:L1 C 30.4
23 49 69 P 19 9:L1 G 3.6
24 49 69 P 20 10:L1 C 24.3
25 50 70 H 20 10:L1 C 2.6
26 51 71 W 19 9:L1 G 12.5
27 51 71 W 20 10:L1 C 12.2

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_D; 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% (16/16).

    Identities = 31% (5/16), Positive = 50% (8/16), Gaps = 0% (0/16).

    Query: 87 EMAEQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEK 146

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

    3oda_D: 23 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 80

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


    Query: 147 LERARATTKKIEDLTELEGWEELEDNEK 174

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

    3oda_D: 81 GHSIRHPDVEVDGFSELR-WDDQQKVKK 107

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


    Download alignment FASTA file