Interaction between Poly [ADP-ribose] polymerase 1 (3od8_F) and Nucleic acid (3od8_M_N)

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_F

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 116 (26 missing in structure)

  • Chain B: 3od8_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: 468.51 Å2

Number of inter-residue contacts at the interface: 30

Number of H-bonds: 4

  • 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_F

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 15 35 K 54.1 36.2 %
    2 16 36 S 27.2 75.7 %
    3 18 38 R 103.2 55.8 %
    4 19 39 A 26.8 100.0 %
    5 20 40 S 17.2 29.6 %
    6 22 42 K 26.3 23.6 %
    7 30 50 K 10.6 8.0 %
    8 34 54 R 18.9 99.3 %
    9 43 63 MSE 14.8 9.2 %
    10 44 64 F 75.5 78.6 %
    11 45 65 D 2.6 1.7 %
    12 46 66 G <0.1 0.1 %
    13 47 67 K 5.6 8.0 %
    14 48 68 V 28.1 64.2 %
    15 49 69 P 29.5 60.8 %
    16 50 70 H 1.6 2.7 %
    17 51 71 W 26.5 73.3 %

  • Interface residues in 3od8_M_N

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 1 1:M1 G 79.7 34.1 %
    2 4 4:M1 G 8.9 5.0 %
    3 5 5:M1 C 32.1 19.9 %
    4 6 6:M1 T 16.1 9.0 %
    5 7 7:M1 T 10.6 5.6 %
    6 17 7:N1 C 0.4 0.2 %
    7 18 8:N1 G 80.2 41.8 %
    8 19 9:N1 G 102.0 63.4 %
    9 20 10:N1 C 138.6 52.7 %

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:N1 G 47.6
2 15 35 K 19 9:N1 G 6.5
3 16 36 S 18 8:N1 G 11.9 H-bond
4 16 36 S 19 9:N1 G 15.3 H-bond
5 18 38 R 4 4:M1 G 8.9
6 18 38 R 5 5:M1 C 32.1
7 18 38 R 6 6:M1 T 16.1
8 18 38 R 17 7:N1 C 0.4
9 18 38 R 18 8:N1 G 20.7
10 18 38 R 19 9:N1 G 23.5
11 18 38 R 20 10:N1 C 1.6
12 19 39 A 19 9:N1 G 19.1
13 19 39 A 20 10:N1 C 7.7
14 20 40 S 20 10:N1 C 17.2 H-bond
15 22 42 K 20 10:N1 C 26.3
16 30 50 K 6 6:M1 T <0.1
17 30 50 K 7 7:M1 T 10.6
18 34 54 R 19 9:N1 G 18.9 H-bond
19 43 63 MSE 1 1:M1 G 14.8
20 44 64 F 1 1:M1 G 62.2
21 44 64 F 20 10:N1 C 13.3
22 45 65 D 1 1:M1 G 2.6
23 46 66 G 1 1:M1 G <0.1
24 47 67 K 20 10:N1 C 5.6
25 48 68 V 20 10:N1 C 28.1
26 49 69 P 19 9:N1 G 4.1
27 49 69 P 20 10:N1 C 25.4
28 50 70 H 20 10:N1 C 1.6
29 51 71 W 19 9:N1 G 14.7
30 51 71 W 20 10:N1 C 11.8

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_F; 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 = 41% (7/17), 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_F: 23 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 80

    dssp: ----EEEEE------E------E-----EEEEEEEE----- -EEEEEEEHHHHHHH


    Query: 147 LERARATTKKIEDLTELEGWEELEDNEK 174

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

    3od8_F: 81 GHSIRHPDVEVDGFSELR-WDDQQKVKK 107

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


    Download alignment FASTA file