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

PDB and SCOP data

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

Title: Structure of Human PARP-1 bound to a DNA double strand break in complex with (2Z)-2-{4-[2-(morpholin-4-yl)ethoxy]benzylidene}-3-oxo-2,3-dihydro-1-benzofuran-7-carboxamide

Release date: 2014-07-02

Resolution: 3.4 Å

  • Chain A: 4oqb_D

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 267 (45 missing in structure)

  • Chain B: 4oqb_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: 540.81 Å2

Number of inter-residue contacts at the interface: 39

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 4oqb_D

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 12 12 E 0.3 1.7 %
    2 15 15 K 52.1 41.8 %
    3 16 16 S 29.0 69.8 %
    4 18 18 R 94.7 50.2 %
    5 19 19 A 35.1 97.4 %
    6 20 20 S 21.3 31.3 %
    7 22 22 K 19.6 19.2 %
    8 34 34 R 18.4 100.0 %
    9 41 41 S 4.5 41.3 %
    10 43 43 M 12.0 6.8 %
    11 44 44 F 70.8 70.9 %
    12 45 45 D 0.1 0.1 %
    13 47 47 K 0.3 0.3 %
    14 48 48 V 33.3 84.6 %
    15 49 49 P 18.9 38.1 %
    16 51 51 W 24.7 73.5 %
    17 259 152 N 11.1 11.5 %
    18 262 155 K 11.4 14.0 %
    19 273 166 P 0.9 7.2 %
    20 274 167 S 40.4 37.7 %
    21 275 168 G 27.8 86.0 %
    22 276 169 E 13.5 14.7 %
    23 277 170 S 0.5 1.1 %

  • Interface residues in 4oqb_M_N

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 23 23:M1 A 70.7 37.8 %
    2 24 24:M1 G 112.6 58.9 %
    3 25 25:M1 G 99.4 63.9 %
    4 26 26:M1 C 131.8 48.8 %
    5 27 1:N1 G 70.3 28.5 %
    6 30 4:N1 T 3.2 1.7 %
    7 31 5:N1 A 29.1 15.5 %
    8 32 6:N1 C 12.6 7.0 %
    9 34 8:N1 G 11.1 5.8 %

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 45.5
3 15 15 K 25 25:M1 G 6.6
4 16 16 S 24 24:M1 G 14.0 H-bond
5 16 16 S 25 25:M1 G 15.0 H-bond
6 18 18 R 23 23:M1 A 4.6
7 18 18 R 24 24:M1 G 24.7
8 18 18 R 25 25:M1 G 20.5
9 18 18 R 30 4:N1 T 3.2
10 18 18 R 31 5:N1 A 29.1
11 18 18 R 32 6:N1 C 12.6
12 19 19 A 25 25:M1 G 24.2
13 19 19 A 26 26:M1 C 11.0
14 20 20 S 26 26:M1 C 21.3 H-bond
15 22 22 K 26 26:M1 C 19.6
16 34 34 R 25 25:M1 G 18.4 H-bond
17 41 41 S 26 26:M1 C 4.5
18 41 41 S 27 1:N1 G <0.1
19 43 43 M 26 26:M1 C 1.8
20 43 43 M 27 1:N1 G 10.3
21 44 44 F 26 26:M1 C 10.9
22 44 44 F 27 1:N1 G 59.9
23 45 45 D 27 1:N1 G 0.1
24 47 47 K 26 26:M1 C 0.3
25 48 48 V 26 26:M1 C 33.3
26 49 49 P 25 25:M1 G 2.5
27 49 49 P 26 26:M1 C 16.4
28 51 51 W 25 25:M1 G 12.0
29 51 51 W 26 26:M1 C 12.7
30 259 152 N 34 8:N1 G 11.1
31 262 155 K 23 23:M1 A 11.4
32 273 166 P 23 23:M1 A 0.9
33 274 167 S 23 23:M1 A 40.0 H-bond
34 274 167 S 24 24:M1 G 0.4
35 275 168 G 23 23:M1 A 13.8
36 275 168 G 24 24:M1 G 14.0
37 276 169 E 23 23:M1 A <0.1
38 276 169 E 24 24:M1 G 13.4
39 277 170 S 24 24:M1 G 0.5

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: 4oqb_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: 70% (16/23).

    Identities = 31% (5/16), Positive = 56% (9/16), Gaps = 0% (0/16).

    Query: 87 EMAEQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEK 146

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

    4oqb_D: 3 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 60

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


    Query: 147 LERARATTKKIEDLTELEGWEE 168

    R +++ +EL W++

    4oqb_D: 61 GHSIRHPDVEVDGFSELR-WDD 81

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


    Download alignment FASTA file