Interaction between Poly [ADP-ribose] polymerase 1 (4opx_D) 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_D

    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: 556.72 Å2

Number of inter-residue contacts at the interface: 40

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_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 12 12 E 0.3 1.8 %
    2 15 15 K 51.9 41.3 %
    3 16 16 S 30.0 70.8 %
    4 18 18 R 100.6 53.7 %
    5 19 19 A 34.9 98.4 %
    6 20 20 S 23.9 34.9 %
    7 22 22 K 22.1 21.9 %
    8 34 34 R 18.7 100.0 %
    9 41 41 S 4.8 43.2 %
    10 43 43 M 14.5 8.2 %
    11 44 44 F 69.8 70.8 %
    12 45 45 D 0.3 0.2 %
    13 47 47 K 0.6 0.5 %
    14 48 48 V 33.9 87.6 %
    15 49 49 P 20.1 40.4 %
    16 50 50 H 0.5 1.0 %
    17 51 51 W 26.6 75.1 %
    18 259 152 N 10.8 11.3 %
    19 262 155 K 9.9 12.2 %
    20 273 166 P 0.8 6.6 %
    21 274 167 S 39.5 37.4 %
    22 275 168 G 28.7 85.3 %
    23 276 169 E 12.6 14.0 %
    24 277 170 S 0.9 1.8 %

  • Interface residues in 4opx_M_N

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 23 23:M1 A 71.8 38.3 %
    2 24 24:M1 G 114.1 60.0 %
    3 25 25:M1 G 99.8 64.9 %
    4 26 26:M1 C 136.8 50.9 %
    5 27 1:N1 G 73.5 29.9 %
    6 30 4:N1 T 3.8 2.0 %
    7 31 5:N1 A 32.7 17.4 %
    8 32 6:N1 C 13.4 7.5 %
    9 34 8:N1 G 10.8 5.7 %
    10 35 9:N1 G <0.1 0.0 %

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 12 12 E 25 25:M1 G 0.3
2 15 15 K 24 24:M1 G 46.9
3 15 15 K 25 25:M1 G 5.0
4 16 16 S 24 24:M1 G 15.3 H-bond
5 16 16 S 25 25:M1 G 14.7 H-bond
6 18 18 R 23 23:M1 A 6.1
7 18 18 R 24 24:M1 G 25.1
8 18 18 R 25 25:M1 G 19.5
9 18 18 R 30 4:N1 T 3.8
10 18 18 R 31 5:N1 A 32.7
11 18 18 R 32 6:N1 C 13.4
12 19 19 A 25 25:M1 G 25.5
13 19 19 A 26 26:M1 C 9.4
14 20 20 S 26 26:M1 C 23.9 H-bond
15 22 22 K 26 26:M1 C 22.1
16 34 34 R 25 25:M1 G 18.7 H-bond
17 41 41 S 26 26:M1 C 4.5
18 41 41 S 27 1:N1 G 0.3
19 43 43 M 26 26:M1 C 2.1
20 43 43 M 27 1:N1 G 12.4
21 44 44 F 26 26:M1 C 9.3
22 44 44 F 27 1:N1 G 60.5
23 45 45 D 27 1:N1 G 0.3
24 47 47 K 26 26:M1 C 0.6
25 48 48 V 26 26:M1 C 33.9
26 49 49 P 25 25:M1 G 2.4
27 49 49 P 26 26:M1 C 17.7
28 50 50 H 26 26:M1 C 0.5
29 51 51 W 25 25:M1 G 13.7
30 51 51 W 26 26:M1 C 12.8
31 259 152 N 34 8:N1 G 10.8
32 259 152 N 35 9:N1 G <0.1
33 262 155 K 23 23:M1 A 9.9
34 273 166 P 23 23:M1 A 0.8
35 274 167 S 23 23:M1 A 39.5 H-bond
36 275 168 G 23 23:M1 A 15.3
37 275 168 G 24 24:M1 G 13.3
38 276 169 E 23 23:M1 A <0.1
39 276 169 E 24 24:M1 G 12.6
40 277 170 S 24 24:M1 G 0.9

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_D; 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: 71% (17/24).

    Identities = 29% (5/17), 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 ++

    4opx_D: 3 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 60

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


    Query: 147 LERARATTKKIEDLTELEGWEE 168

    R +++ +EL W++

    4opx_D: 61 GHSIRHPDVEVDGFSELR-WDD 81

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


    Download alignment FASTA file