Interaction between Poly [ADP-ribose] polymerase 1 (4oqb_A) 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_A

    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: 592.05 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 4oqb_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 12 12 E <0.1 0.6 %
    2 15 15 K 57.3 46.8 %
    3 16 16 S 29.5 71.0 %
    4 18 18 R 115.9 64.9 %
    5 19 19 A 35.1 96.8 %
    6 20 20 S 21.6 31.7 %
    7 22 22 K 21.1 20.7 %
    8 30 30 K 5.0 4.3 %
    9 34 34 R 18.2 100.0 %
    10 41 41 S 5.7 51.0 %
    11 43 43 M 14.1 7.9 %
    12 44 44 F 70.0 70.0 %
    13 47 47 K 0.8 0.7 %
    14 48 48 V 34.0 88.3 %
    15 49 49 P 21.2 42.6 %
    16 50 50 H 0.6 1.3 %
    17 51 51 W 24.5 72.8 %
    18 258 151 T 3.6 7.3 %
    19 259 152 N 16.5 17.5 %
    20 262 155 K 10.8 13.3 %
    21 273 166 P <0.1 0.8 %
    22 274 167 S 40.3 36.1 %
    23 275 168 G 28.0 90.5 %
    24 276 169 E 14.0 15.4 %
    25 277 170 S 4.2 8.2 %

  • Interface residues in 4oqb_M_N

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 1 1:M1 G 71.1 30.0 %
    2 4 4:M1 T 3.6 1.9 %
    3 5 5:M1 A 37.3 20.2 %
    4 6 6:M1 C 23.4 13.1 %
    5 7 7:M1 C 5.0 2.9 %
    6 8 8:M1 G 8.0 4.0 %
    7 9 9:M1 G 12.1 7.8 %
    8 49 23:N1 A 76.6 41.0 %
    9 50 24:N1 G 116.6 62.0 %
    10 51 25:N1 G 99.4 63.9 %
    11 52 26:N1 C 138.8 51.4 %

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 <0.1
2 15 15 K 50 24:N1 G 50.4
3 15 15 K 51 25:N1 G 6.8
4 16 16 S 6 6:M1 C 0.3
5 16 16 S 50 24:N1 G 14.3 H-bond
6 16 16 S 51 25:N1 G 14.9 H-bond
7 18 18 R 4 4:M1 T 3.6
8 18 18 R 5 5:M1 A 37.3
9 18 18 R 6 6:M1 C 23.1
10 18 18 R 49 23:N1 A 9.2
11 18 18 R 50 24:N1 G 22.0
12 18 18 R 51 25:N1 G 20.6
13 19 19 A 51 25:N1 G 24.6
14 19 19 A 52 26:N1 C 10.4
15 20 20 S 52 26:N1 C 21.6 H-bond
16 22 22 K 52 26:N1 C 21.1
17 30 30 K 7 7:M1 C 5.0
18 34 34 R 51 25:N1 G 18.2 H-bond
19 41 41 S 1 1:M1 G <0.1
20 41 41 S 52 26:N1 C 5.6
21 43 43 M 1 1:M1 G 12.0
22 43 43 M 52 26:N1 C 2.1
23 44 44 F 1 1:M1 G 59.1
24 44 44 F 52 26:N1 C 11.0
25 47 47 K 52 26:N1 C 0.8
26 48 48 V 52 26:N1 C 34.0
27 49 49 P 51 25:N1 G 2.6
28 49 49 P 52 26:N1 C 18.7
29 50 50 H 52 26:N1 C 0.6
30 51 51 W 51 25:N1 G 11.5
31 51 51 W 52 26:N1 C 12.9
32 258 151 T 8 8:M1 G 3.6
33 259 152 N 8 8:M1 G 4.4
34 259 152 N 9 9:M1 G 12.1
35 262 155 K 49 23:N1 A 10.8
36 273 166 P 49 23:N1 A <0.1
37 274 167 S 49 23:N1 A 34.7 H-bond
38 274 167 S 50 24:N1 G 5.5
39 275 168 G 49 23:N1 A 17.2
40 275 168 G 50 24:N1 G 10.8
41 276 169 E 49 23:N1 A 4.7
42 276 169 E 50 24:N1 G 9.4
43 277 170 S 50 24:N1 G 4.2

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: 4oqb_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: 68% (17/25).

    Identities = 35% (6/17), 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 ++

    4oqb_A: 3 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 60

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


    Query: 147 LERARATTKKIEDLTELEGWEE 168

    R +++ +EL W++

    4oqb_A: 61 GHSIRHPDVEVDGFSELR-WDD 81

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


    Download alignment FASTA file