Interaction between Poly [ADP-ribose] polymerase 1 (3oda_E) 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_E

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 116 (30 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: 488.40 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_E

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 12 32 E 0.2 0.8 %
    2 15 35 K 56.1 35.8 %
    3 16 36 S 27.3 70.4 %
    4 18 38 R 122.7 65.4 %
    5 19 39 A 26.4 100.0 %
    6 20 40 S 22.1 33.3 %
    7 22 42 K 24.2 21.9 %
    8 30 50 K 3.6 2.8 %
    9 34 54 R 20.3 99.9 %
    10 43 63 M 49.1 29.8 %
    11 44 64 F 64.3 64.6 %
    12 45 65 D <0.1 0.0 %
    13 47 67 K 0.1 0.1 %
    14 48 68 V 28.4 78.0 %
    15 49 69 P 18.8 43.7 %
    16 50 70 H <0.1 0.1 %
    17 51 71 W 24.5 77.8 %

  • Interface residues in 3oda_M_N

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 7 7:M1 A 6.6 3.8 %
    2 8 8:M1 G 91.3 46.7 %
    3 9 9:M1 G 100.1 66.2 %
    4 10 10:M1 C 155.4 57.5 %
    5 11 1:N1 G 72.9 31.8 %
    6 14 4:N1 T 3.5 1.9 %
    7 15 5:N1 G 42.9 23.3 %
    8 16 6:N1 C 12.2 7.7 %
    9 17 7:N1 A 3.6 2.1 %

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:M1 G 0.2
2 15 35 K 8 8:M1 G 48.1
3 15 35 K 9 9:M1 G 8.1
4 16 36 S 8 8:M1 G 11.9
5 16 36 S 9 9:M1 G 15.4 H-bond
6 18 38 R 7 7:M1 A 6.6
7 18 38 R 8 8:M1 G 31.4
8 18 38 R 9 9:M1 G 24.1
9 18 38 R 10 10:M1 C 2.0
10 18 38 R 14 4:N1 T 3.5
11 18 38 R 15 5:N1 G 42.9
12 18 38 R 16 6:N1 C 12.2
13 19 39 A 9 9:M1 G 19.4
14 19 39 A 10 10:M1 C 7.0
15 20 40 S 10 10:M1 C 22.1 H-bond
16 22 42 K 10 10:M1 C 24.2
17 30 50 K 17 7:N1 A 3.6
18 34 54 R 9 9:M1 G 20.3 H-bond
19 43 63 M 10 10:M1 C 30.5
20 43 63 M 11 1:N1 G 18.7
21 44 64 F 10 10:M1 C 10.1
22 44 64 F 11 1:N1 G 54.2
23 45 65 D 11 1:N1 G <0.1
24 47 67 K 10 10:M1 C 0.1
25 48 68 V 10 10:M1 C 28.4
26 49 69 P 9 9:M1 G 0.4
27 49 69 P 10 10:M1 C 18.4
28 50 70 H 10 10:M1 C <0.1
29 51 71 W 9 9:M1 G 12.1
30 51 71 W 10 10:M1 C 12.5

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_E; 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 = 35% (6/17), 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_E: 23 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 80

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


    Query: 147 LERARATTKKIEDLTELEGWEELEDNEK 174

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

    3oda_E: 81 GHSIRHPDVEVDGFSELR-WDDQQKVKK 107

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


    Download alignment FASTA file