Interaction between Poly [ADP-ribose] polymerase 1 (4opx_A) and DNA (26-MER) (4opx_M_N)

PDB and SCOP data

PDB ID: 4opx (all binary interactions in this PDB entry)

Title: Structure of Human PARP-1 bound to a DNA double strand break in complex with (2R)-5-fluoro-2-methyl-2,3-dihydro-1-benzofuran-7-carboxamide

Release date: 2014-07-02

Resolution: 3.3 Å

  • Chain A: 4opx_A

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 267 (45 missing in structure)

  • Chain B: 4opx_M_N

    Title: DNA (26-MER)

    Number of residues: 52

    Note: Residues of nucleic acid domain are renumbered to avoid repeating the same residue numbers from different PDB chains.

Buried interface area: 599.41 Å2

Number of inter-residue contacts at the interface: 43

Number of H-bonds: 5

  • Pairwise interaction

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    Download PyMOL visualization script

  • Biological assembly

    Heteromer, 2 proteins, 1 nucleic acid.

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Create a structural model for this interaction

  • Interface residues in 4opx_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 12 12 E 0.2 1.1 %
    2 15 15 K 56.8 46.4 %
    3 16 16 S 31.0 73.6 %
    4 17 17 G 1.8 4.2 %
    5 18 18 R 118.7 67.2 %
    6 19 19 A 34.6 97.9 %
    7 20 20 S 23.2 33.9 %
    8 22 22 K 22.4 22.3 %
    9 30 30 K 6.5 5.6 %
    10 34 34 R 18.1 100.0 %
    11 41 41 S 5.7 51.2 %
    12 43 43 M 15.1 8.5 %
    13 44 44 F 68.7 68.9 %
    14 47 47 K 0.8 0.6 %
    15 48 48 V 34.3 89.7 %
    16 49 49 P 21.6 43.1 %
    17 50 50 H 1.2 2.6 %
    18 51 51 W 25.7 73.9 %
    19 258 151 T 3.9 8.2 %
    20 259 152 N 15.2 16.0 %
    21 262 155 K 9.3 11.4 %
    22 274 167 S 39.1 35.3 %
    23 275 168 G 28.2 88.8 %
    24 276 169 E 13.0 14.5 %
    25 277 170 S 4.1 8.1 %

  • Interface residues in 4opx_M_N

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 1 1:M1 G 71.9 30.4 %
    2 4 4:M1 T 3.9 2.0 %
    3 5 5:M1 A 39.8 21.6 %
    4 6 6:M1 C 25.7 14.4 %
    5 7 7:M1 C 6.5 3.7 %
    6 8 8:M1 G 7.7 3.9 %
    7 9 9:M1 G 11.5 7.3 %
    8 49 23:N1 A 74.3 39.7 %
    9 50 24:N1 G 116.9 62.2 %
    10 51 25:N1 G 99.7 64.5 %
    11 52 26:N1 C 141.5 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 12 12 E 51 25:N1 G 0.2
2 15 15 K 50 24:N1 G 50.3
3 15 15 K 51 25:N1 G 6.5
4 16 16 S 6 6:M1 C 1.2
5 16 16 S 50 24:N1 G 14.9 H-bond
6 16 16 S 51 25:N1 G 14.9 H-bond
7 17 17 G 6 6:M1 C 1.8
8 18 18 R 4 4:M1 T 3.9
9 18 18 R 5 5:M1 A 39.8
10 18 18 R 6 6:M1 C 22.8
11 18 18 R 49 23:N1 A 9.9
12 18 18 R 50 24:N1 G 22.3
13 18 18 R 51 25:N1 G 20.1
14 19 19 A 51 25:N1 G 25.0
15 19 19 A 52 26:N1 C 9.6
16 20 20 S 52 26:N1 C 23.2 H-bond
17 22 22 K 52 26:N1 C 22.4
18 30 30 K 7 7:M1 C 6.5
19 34 34 R 51 25:N1 G 18.1 H-bond
20 41 41 S 1 1:M1 G 0.2
21 41 41 S 52 26:N1 C 5.5
22 43 43 M 1 1:M1 G 12.8
23 43 43 M 52 26:N1 C 2.3
24 44 44 F 1 1:M1 G 58.8
25 44 44 F 52 26:N1 C 9.9
26 47 47 K 52 26:N1 C 0.8
27 48 48 V 52 26:N1 C 34.3
28 49 49 P 51 25:N1 G 2.5
29 49 49 P 52 26:N1 C 19.1
30 50 50 H 52 26:N1 C 1.2
31 51 51 W 51 25:N1 G 12.6
32 51 51 W 52 26:N1 C 13.1
33 258 151 T 8 8:M1 G 3.9
34 259 152 N 8 8:M1 G 3.7
35 259 152 N 9 9:M1 G 11.5
36 262 155 K 49 23:N1 A 9.3
37 274 167 S 49 23:N1 A 33.7 H-bond
38 274 167 S 50 24:N1 G 5.5
39 275 168 G 49 23:N1 A 17.3
40 275 168 G 50 24:N1 G 11.0
41 276 169 E 49 23:N1 A 4.2
42 276 169 E 50 24:N1 G 8.8
43 277 170 S 50 24:N1 G 4.1

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: 4opx_A; Poly [ADP-ribose] polymerase 1

    Alignment data:

    Expectation value = 1.38e-4, Score = 48 bits (112),

    Identities = 32% (26/82), Positive = 54% (44/82), Gaps = 4% (3/82).

    Interface alignment data:

    Interface residues in alignment: 72% (18/25).

    Identities = 39% (7/18), Positive = 56% (10/18), Gaps = 0% (0/18).

    Query: 87 EMAEQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEK 146

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

    4opx_A: 3 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 60

    dssp: ---EEEEE------E------E-----EEEEEEEE----- -EEEEEEE--HHH--


    Query: 147 LERARATTKKIEDLTELEGWEE 168

    R +++ +EL W++

    4opx_A: 61 GHSIRHPDVEVDGFSELR-WDD 81

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


    Download alignment FASTA file