Interaction between Poly [ADP-ribose] polymerase 1 (3od8_B) and Nucleic acid (3od8_I_J)

PDB and SCOP data

PDB ID: 3od8 (all binary interactions in this PDB entry)

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

Release date: 2011-01-12

Resolution: 2.4 Å

  • Chain A: 3od8_B

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 116 (29 missing in structure)

  • Chain B: 3od8_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: 449.00 Å2

Number of inter-residue contacts at the interface: 26

Number of H-bonds: 5

  • 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 3od8_B

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 15 35 K 53.3 35.2 %
    2 16 36 S 27.4 77.6 %
    3 18 38 R 109.5 56.7 %
    4 19 39 A 26.6 100.0 %
    5 20 40 S 15.8 28.5 %
    6 22 42 K 28.2 25.0 %
    7 34 54 R 19.1 99.0 %
    8 43 63 MSE 10.4 6.8 %
    9 44 64 F 68.6 68.4 %
    10 47 67 K 5.4 8.2 %
    11 48 68 V 29.2 59.8 %
    12 49 69 P 27.5 57.5 %
    13 50 70 H 2.8 4.4 %
    14 51 71 W 25.1 75.9 %

  • Interface residues in 3od8_I_J

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 1 1:I1 G 70.0 30.2 %
    2 4 4:I1 G 8.0 4.5 %
    3 5 5:I1 C 33.5 21.2 %
    4 6 6:I1 T 17.2 9.4 %
    5 17 7:J1 C 1.1 0.6 %
    6 18 8:J1 G 81.1 42.2 %
    7 19 9:J1 G 100.1 64.5 %
    8 20 10:J1 C 137.9 53.0 %

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 44.9
2 15 35 K 19 9:J1 G 8.4
3 16 36 S 18 8:J1 G 11.3 H-bond
4 16 36 S 19 9:J1 G 16.1 H-bond
5 18 38 R 4 4:I1 G 8.0
6 18 38 R 5 5:I1 C 33.5
7 18 38 R 6 6:I1 T 17.2
8 18 38 R 17 7:J1 C 1.1
9 18 38 R 18 8:J1 G 24.9
10 18 38 R 19 9:J1 G 23.0
11 18 38 R 20 10:J1 C 1.8
12 19 39 A 19 9:J1 G 19.2
13 19 39 A 20 10:J1 C 7.5
14 20 40 S 20 10:J1 C 15.8 H-bond
15 22 42 K 20 10:J1 C 28.2 H-bond
16 34 54 R 19 9:J1 G 19.1 H-bond
17 43 63 MSE 1 1:I1 G 10.4
18 44 64 F 1 1:I1 G 59.6
19 44 64 F 20 10:J1 C 9.0
20 47 67 K 20 10:J1 C 5.4
21 48 68 V 20 10:J1 C 29.2
22 49 69 P 19 9:J1 G 1.8
23 49 69 P 20 10:J1 C 25.7
24 50 70 H 20 10:J1 C 2.8
25 51 71 W 19 9:J1 G 12.6
26 51 71 W 20 10:J1 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: 3od8_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% (14/14).

    Identities = 36% (5/14), Positive = 43% (6/14), Gaps = 0% (0/14).

    Query: 87 EMAEQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEK 146

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

    3od8_B: 23 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 80

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


    Query: 147 LERARATTKKIEDLTELEGWEELEDNEK 174

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

    3od8_B: 81 GHSIRHPDVEVDGFSELR-WDDQQKVKK 107

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


    Download alignment FASTA file