Interaction between Poly [ADP-ribose] polymerase 1 (3od8_A) 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_A

    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: 487.36 Å2

Number of inter-residue contacts at the interface: 29

Number of H-bonds: 4

  • 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 3od8_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 15 35 K 57.6 36.8 %
    2 16 36 S 25.9 69.4 %
    3 18 38 R 120.1 64.0 %
    4 19 39 A 25.5 100.0 %
    5 20 40 S 22.0 33.3 %
    6 22 42 K 26.7 24.4 %
    7 34 54 R 18.5 99.7 %
    8 41 61 S 1.0 5.1 %
    9 43 63 MSE 26.4 16.8 %
    10 44 64 F 64.3 64.4 %
    11 47 67 K 1.4 1.8 %
    12 48 68 V 33.3 85.3 %
    13 49 69 P 28.0 72.5 %
    14 50 70 H 9.5 14.3 %
    15 51 71 W 27.2 87.7 %

  • Interface residues in 3od8_I_J

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 7 7:I1 T 4.3 2.3 %
    2 8 8:I1 G 87.6 46.6 %
    3 9 9:I1 G 101.1 66.0 %
    4 10 10:I1 G 162.4 59.6 %
    5 11 1:J1 C 67.5 32.2 %
    6 12 2:J1 C 4.8 2.9 %
    7 14 4:J1 A 4.0 2.4 %
    8 15 5:J1 A 33.3 19.3 %
    9 16 6:J1 G 22.4 13.0 %

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 8 8:I1 G 49.5
2 15 35 K 9 9:I1 G 8.1
3 16 36 S 8 8:I1 G 10.7
4 16 36 S 9 9:I1 G 15.2 H-bond
5 18 38 R 7 7:I1 T 4.3
6 18 38 R 8 8:I1 G 27.4
7 18 38 R 9 9:I1 G 26.2
8 18 38 R 10 10:I1 G 2.5
9 18 38 R 14 4:J1 A 4.0
10 18 38 R 15 5:J1 A 33.3
11 18 38 R 16 6:J1 G 22.4
12 19 39 A 9 9:I1 G 17.5
13 19 39 A 10 10:I1 G 8.0
14 20 40 S 10 10:I1 G 22.0 H-bond
15 22 42 K 10 10:I1 G 26.7 H-bond
16 34 54 R 9 9:I1 G 18.5 H-bond
17 41 61 S 10 10:I1 G 1.0
18 43 63 MSE 10 10:I1 G 8.2
19 43 63 MSE 11 1:J1 C 13.4
20 43 63 MSE 12 2:J1 C 4.8
21 44 64 F 10 10:I1 G 10.2
22 44 64 F 11 1:J1 C 54.1
23 47 67 K 10 10:I1 G 1.4
24 48 68 V 10 10:I1 G 33.3
25 49 69 P 9 9:I1 G 1.1
26 49 69 P 10 10:I1 G 26.9
27 50 70 H 10 10:I1 G 9.5
28 51 71 W 9 9:I1 G 14.6
29 51 71 W 10 10:I1 G 12.6

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_A; 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 ++

    3od8_A: 23 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 80

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


    Query: 147 LERARATTKKIEDLTELEGWEELEDNEK 174

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

    3od8_A: 81 GHSIRHPDVEVDGFSELR-WDDQQKVKK 107

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


    Download alignment FASTA file