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

PDB and SCOP data

PDB ID: 4oqa (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-(2,4-dihydroxybenzylidene)-3-oxo-2,3-dihydro-1-benzofuran-7-carboxamide

Release date: 2014-07-02

Resolution: 3.6 Å

  • Chain A: 4oqa_A

    Title: Poly [ADP-ribose] polymerase 1

    Source organism: Homo sapiens

    Number of residues: 267 (45 missing in structure)

  • Chain B: 4oqa_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: 591.39 Å2

Number of inter-residue contacts at the interface: 44

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 4oqa_A

    No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, %
    1 12 12 E 0.2 1.0 %
    2 15 15 K 56.4 46.1 %
    3 16 16 S 30.2 72.3 %
    4 17 17 G 0.9 2.2 %
    5 18 18 R 118.2 66.5 %
    6 19 19 A 34.6 97.1 %
    7 20 20 S 20.8 30.7 %
    8 22 22 K 20.5 20.3 %
    9 30 30 K 6.4 5.6 %
    10 34 34 R 17.7 100.0 %
    11 41 41 S 5.7 51.3 %
    12 43 43 M 14.9 8.4 %
    13 44 44 F 68.6 68.1 %
    14 47 47 K 0.6 0.5 %
    15 48 48 V 34.2 88.4 %
    16 49 49 P 19.9 39.9 %
    17 50 50 H 0.8 1.7 %
    18 51 51 W 24.4 73.7 %
    19 258 151 T 6.4 12.8 %
    20 259 152 N 17.0 17.9 %
    21 262 155 K 8.9 11.0 %
    22 273 166 P <0.1 0.0 %
    23 274 167 S 39.3 35.8 %
    24 275 168 G 28.5 88.4 %
    25 276 169 E 12.3 13.6 %
    26 277 170 S 4.0 7.8 %

  • Interface residues in 4oqa_M_N

    No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, %
    1 1 1:M1 G 70.2 29.3 %
    2 4 4:M1 T 3.8 2.0 %
    3 5 5:M1 A 39.5 21.4 %
    4 6 6:M1 C 25.2 14.1 %
    5 7 7:M1 C 6.4 3.7 %
    6 8 8:M1 G 11.3 5.7 %
    7 9 9:M1 G 12.1 7.8 %
    8 49 23:N1 A 71.1 37.8 %
    9 50 24:N1 G 115.5 61.4 %
    10 51 25:N1 G 99.1 63.9 %
    11 52 26:N1 C 137.3 50.8 %

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 51 25:N1 G 0.2
2 15 15 K 50 24:N1 G 48.7
3 15 15 K 51 25:N1 G 7.7
4 16 16 S 6 6:M1 C 1.1
5 16 16 S 50 24:N1 G 14.0 H-bond
6 16 16 S 51 25:N1 G 15.1 H-bond
7 17 17 G 6 6:M1 C 0.9
8 18 18 R 4 4:M1 T 3.8
9 18 18 R 5 5:M1 A 39.5
10 18 18 R 6 6:M1 C 23.1
11 18 18 R 49 23:N1 A 8.7
12 18 18 R 50 24:N1 G 22.3
13 18 18 R 51 25:N1 G 20.9
14 19 19 A 51 25:N1 G 23.5
15 19 19 A 52 26:N1 C 11.1
16 20 20 S 52 26:N1 C 20.8 H-bond
17 22 22 K 52 26:N1 C 20.5
18 30 30 K 7 7:M1 C 6.4
19 34 34 R 51 25:N1 G 17.7 H-bond
20 41 41 S 1 1:M1 G <0.1
21 41 41 S 52 26:N1 C 5.6
22 43 43 M 1 1:M1 G 12.4
23 43 43 M 52 26:N1 C 2.5
24 44 44 F 1 1:M1 G 57.7
25 44 44 F 52 26:N1 C 10.9
26 47 47 K 52 26:N1 C 0.6
27 48 48 V 52 26:N1 C 34.2
28 49 49 P 51 25:N1 G 2.6
29 49 49 P 52 26:N1 C 17.3
30 50 50 H 52 26:N1 C 0.8
31 51 51 W 51 25:N1 G 11.4
32 51 51 W 52 26:N1 C 13.0
33 258 151 T 8 8:M1 G 6.4
34 259 152 N 8 8:M1 G 4.9
35 259 152 N 9 9:M1 G 12.1
36 262 155 K 49 23:N1 A 8.9
37 273 166 P 49 23:N1 A <0.1
38 274 167 S 49 23:N1 A 32.8 H-bond
39 274 167 S 50 24:N1 G 6.5
40 275 168 G 49 23:N1 A 17.3
41 275 168 G 50 24:N1 G 11.2
42 276 169 E 49 23:N1 A 3.4
43 276 169 E 50 24:N1 G 8.9
44 277 170 S 50 24:N1 G 4.0

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: 4oqa_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: 69% (18/26).

    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 ++

    4oqa_A: 3 ESSDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKV 60

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


    Query: 147 LERARATTKKIEDLTELEGWEE 168

    R +++ +EL W++

    4oqa_A: 61 GHSIRHPDVEVDGFSELR-WDD 81

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


    Download alignment FASTA file