Interaction between POLY [ADP-RIBOSE] POLYMERASE 1 (4av1_C) and Nucleic acid (4av1_X_Y)
PDB and SCOP data
PDB ID: 4av1 (all binary interactions in this PDB entry)
Title: Crystal structure of the human PARP-1 DNA binding domain in complex with DNA
Release date: 2012-06-13
Resolution: 3.1 Å
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Chain A: 4av1_C
Title: POLY [ADP-RIBOSE] POLYMERASE 1
Source organism: Homo sapiens
Number of residues: 223 (138 missing in structure)
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Chain B: 4av1_X_Y
Title: Nucleic acid
Source organism: synthetic construct
Number of residues: 24
Note: Residues of nucleic acid domain are renumbered to avoid repeating the same residue numbers from different PDB chains.
Structural properties
Hetero-dimer interface properties
Buried interface area: 327.17 Å2
Number of inter-residue contacts at the interface: 24
Number of H-bonds: 2
Experimental structure
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Pairwise interaction
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Biological assembly
Homomer, 4 proteins, 1 nucleic acid.
Interface structure modeling
Residues at the interaction interface
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Interface residues in 4av1_C
No. Residue no. in structure Residue no. in sequence Residue name Buried ASA, Å2 Buried ASA, % 1 15 36 K 47.7 29.8 % 2 16 37 S 41.8 86.1 % 3 18 39 R 109.7 55.9 % 4 19 40 A 18.9 92.9 % 5 20 41 S 23.6 41.0 % 6 22 43 K 26.5 25.4 % 7 34 55 R 18.4 99.4 % 8 48 69 V 2.7 4.8 % 9 49 70 P 8.6 18.2 % 10 50 71 H <0.1 0.0 % 11 51 72 W 29.3 78.3 %
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Interface residues in 4av1_X_Y
No. Residue no. in structure PDB residue no. Residue name Buried ASA, Å2 Buried ASA, % 1 9 9:X1 C 17.3 10.2 % 2 10 10:X1 A 13.8 7.9 % 3 11 11:X1 T 3.6 1.9 % 4 13 1:Y1 T 22.6 7.9 % 5 14 2:Y1 A 121.1 63.4 % 6 15 3:Y1 A 102.9 59.7 % 7 16 4:Y1 T 45.9 23.8 %
Inter-residue contacts at the interaction interface
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 |
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1 | 15 | 36 | K | 15 | 3:Y1 | A | 30.5 | |
2 | 15 | 36 | K | 16 | 4:Y1 | T | 17.1 | |
3 | 16 | 37 | S | 15 | 3:Y1 | A | 29.0 | |
4 | 16 | 37 | S | 16 | 4:Y1 | T | 12.8 | |
5 | 18 | 39 | R | 9 | 9:X1 | C | 17.3 | |
6 | 18 | 39 | R | 10 | 10:X1 | A | 13.8 | |
7 | 18 | 39 | R | 11 | 11:X1 | T | 3.6 | |
8 | 18 | 39 | R | 14 | 2:Y1 | A | 38.6 | |
9 | 18 | 39 | R | 15 | 3:Y1 | A | 20.6 | |
10 | 18 | 39 | R | 16 | 4:Y1 | T | 15.9 | |
11 | 19 | 40 | A | 14 | 2:Y1 | A | 14.9 | |
12 | 19 | 40 | A | 15 | 3:Y1 | A | 3.9 | |
13 | 20 | 41 | S | 13 | 1:Y1 | T | 3.8 | |
14 | 20 | 41 | S | 14 | 2:Y1 | A | 19.8 | H-bond |
15 | 22 | 43 | K | 13 | 1:Y1 | T | 13.9 | |
16 | 22 | 43 | K | 14 | 2:Y1 | A | 12.6 | |
17 | 34 | 55 | R | 14 | 2:Y1 | A | 2.2 | |
18 | 34 | 55 | R | 15 | 3:Y1 | A | 16.2 | H-bond |
19 | 48 | 69 | V | 13 | 1:Y1 | T | 2.7 | |
20 | 49 | 70 | P | 13 | 1:Y1 | T | 2.2 | |
21 | 49 | 70 | P | 14 | 2:Y1 | A | 6.4 | |
22 | 50 | 71 | H | 14 | 2:Y1 | A | <0.1 | |
23 | 51 | 72 | W | 14 | 2:Y1 | A | 26.6 | |
24 | 51 | 72 | W | 15 | 3:Y1 | A | 2.7 |
Sequence alignments
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Query protein: sp|P49916|DNLI3_HUMAN DNA ligase 3 OS=Homo sapiens GN=LIG3 PE=1 SV=2
Result domain: 4av1_C; POLY [ADP-RIBOSE] POLYMERASE 1
Alignment data:
Expectation value = 7.89e-5, Score = 48 bits (113),
Identities = 29% (29/100), Positive = 50% (50/100), Gaps = 6% (6/100).
Interface alignment data:
Interface residues in alignment: 100% (11/11).
Identities = 45% (5/11), Positive = 55% (6/11), Gaps = 0% (0/11).
Query: 89 AEQRFCVDYAKRGTAGCKKCKEKIVKGVCRIGKVVPNPFSESGGDMKEWYHIKCMFEKLE 148
+++ + V+YAK G A CKKC E I K R+ +V +P + G + WYH C ++
4av1_C: 26 SDKLYRVEYAKSGRASCKKCSESIPKDSLRMAIMVQSPMFD--GKVPHWYHFSCFWKVGH 83
dssp: ---EEEEE------E------E-----EEEEEEEE----- -EEEEEEEHHHHHHH--
Query: 149 RARATTKKIEDLTELEGWEELEDNEKEQITQHIADLSSKA 188
R +++ +EL W +D +K + T ++ K
4av1_C: 84 SIRHPDVEVDGFSELR-W---DDQQKVKKTAEAGGVTGKG 119
dssp: ----HHHHEE-HHH-- H HHHHHHHHHH-