Interaction between Poly [ADP-ribose] polymerase 1 (3od8_C) and Nucleic acid (3od8_K_L)

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_C

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 116 (29 missing in structure)

  • Chain B: 3od8_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: 464.91 Å2

Number of inter-residue contacts at the interface: 30

Number of H-bonds: 3

  • 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_C

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 12 32 E 0.1 0.6 %
    2 15 35 K 58.1 39.4 %
    3 16 36 S 26.6 79.5 %
    4 18 38 R 104.9 56.1 %
    5 19 39 A 24.2 100.0 %
    6 20 40 S 21.0 31.3 %
    7 22 42 K 21.8 20.0 %
    8 30 50 K 2.3 1.8 %
    9 34 54 R 20.0 100.0 %
    10 43 63 MSE 43.7 28.8 %
    11 44 64 F 65.1 68.4 %
    12 45 65 D <0.1 0.1 %
    13 47 67 K 1.0 0.9 %
    14 48 68 V 25.8 85.8 %
    15 49 69 P 23.8 47.2 %
    16 50 70 H <0.1 0.0 %
    17 51 71 W 26.5 83.3 %

  • Interface residues in 3od8_K_L

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 7 7:K1 T 2.3 1.3 %
    2 8 8:K1 G 82.0 42.9 %
    3 9 9:K1 G 104.6 64.3 %
    4 10 10:K1 G 167.1 59.8 %
    5 11 1:L1 C 51.6 25.4 %
    6 14 4:L1 A 4.2 2.3 %
    7 15 5:L1 A 35.8 21.3 %
    8 16 6:L1 G 15.0 8.7 %
    9 17 7:L1 C 2.3 1.4 %

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 0.1
2 15 35 K 8 8:K1 G 49.9
3 15 35 K 9 9:K1 G 8.2
4 16 36 S 8 8:K1 G 10.8
5 16 36 S 9 9:K1 G 15.8 H-bond
6 18 38 R 7 7:K1 T 2.3
7 18 38 R 8 8:K1 G 21.4
8 18 38 R 9 9:K1 G 24.9
9 18 38 R 10 10:K1 G 1.3
10 18 38 R 14 4:L1 A 4.2
11 18 38 R 15 5:L1 A 35.8
12 18 38 R 16 6:L1 G 15.0
13 19 39 A 9 9:K1 G 18.0
14 19 39 A 10 10:K1 G 6.3
15 20 40 S 10 10:K1 G 21.0 H-bond
16 22 42 K 10 10:K1 G 21.8
17 30 50 K 17 7:L1 C 2.3
18 34 54 R 9 9:K1 G 20.0 H-bond
19 43 63 MSE 10 10:K1 G 40.9
20 43 63 MSE 11 1:L1 C 2.8
21 44 64 F 10 10:K1 G 16.3
22 44 64 F 11 1:L1 C 48.7
23 45 65 D 11 1:L1 C <0.1
24 47 67 K 10 10:K1 G 1.0
25 48 68 V 10 10:K1 G 25.8
26 49 69 P 9 9:K1 G 3.8
27 49 69 P 10 10:K1 G 20.1
28 50 70 H 10 10:K1 G <0.1
29 51 71 W 9 9:K1 G 13.9
30 51 71 W 10 10:K1 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_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 = 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 ++

    3od8_C: 23 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 80

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


    Query: 147 LERARATTKKIEDLTELEGWEELEDNEK 174

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

    3od8_C: 81 GHSIRHPDVEVDGFSELR-WDDQQKVKK 107

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


    Download alignment FASTA file