Interaction between Poly [ADP-ribose] polymerase 1 (3od8_D) 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_D

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 116 (27 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: 461.97 Å2

Number of inter-residue contacts at the interface: 27

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_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 15 35 K 54.3 36.5 %
    2 16 36 S 25.3 79.3 %
    3 18 38 R 109.1 56.7 %
    4 19 39 A 25.5 100.0 %
    5 20 40 S 14.8 27.6 %
    6 22 42 K 29.8 26.6 %
    7 34 54 R 19.9 97.7 %
    8 43 63 MSE 14.4 9.1 %
    9 44 64 F 74.0 75.6 %
    10 45 65 D 1.3 0.8 %
    11 47 67 K 4.9 8.2 %
    12 48 68 V 27.8 56.7 %
    13 49 69 P 32.1 62.2 %
    14 50 70 H 3.3 5.3 %
    15 51 71 W 25.3 79.9 %

  • Interface residues in 3od8_K_L

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 1 1:K1 G 81.1 35.9 %
    2 4 4:K1 G 9.0 5.1 %
    3 5 5:K1 C 33.1 20.3 %
    4 6 6:K1 T 18.2 10.0 %
    5 17 7:L1 C 0.3 0.2 %
    6 18 8:L1 G 79.6 42.2 %
    7 19 9:L1 G 102.0 64.2 %
    8 20 10:L1 C 138.7 53.1 %

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 15 35 K 18 8:L1 G 47.7
2 15 35 K 19 9:L1 G 6.6
3 16 36 S 18 8:L1 G 9.5 H-bond
4 16 36 S 19 9:L1 G 15.8 H-bond
5 18 38 R 4 4:K1 G 9.0
6 18 38 R 5 5:K1 C 33.1
7 18 38 R 6 6:K1 T 18.2
8 18 38 R 17 7:L1 C 0.3
9 18 38 R 18 8:L1 G 22.4
10 18 38 R 19 9:L1 G 24.4
11 18 38 R 20 10:L1 C 1.7
12 19 39 A 19 9:L1 G 18.1
13 19 39 A 20 10:L1 C 7.4
14 20 40 S 20 10:L1 C 14.8 H-bond
15 22 42 K 20 10:L1 C 29.8 H-bond
16 34 54 R 19 9:L1 G 19.9 H-bond
17 43 63 MSE 1 1:K1 G 14.4
18 44 64 F 1 1:K1 G 65.3
19 44 64 F 20 10:L1 C 8.7
20 45 65 D 1 1:K1 G 1.3
21 47 67 K 20 10:L1 C 4.9
22 48 68 V 20 10:L1 C 27.8
23 49 69 P 19 9:L1 G 4.0
24 49 69 P 20 10:L1 C 28.1
25 50 70 H 20 10:L1 C 3.3
26 51 71 W 19 9:L1 G 13.0
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: 3od8_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% (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_D: 23 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 80

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


    Query: 147 LERARATTKKIEDLTELEGWEELEDNEK 174

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

    3od8_D: 81 GHSIRHPDVEVDGFSELR-WDDQQKVKK 107

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


    Download alignment FASTA file