SMTL ID : 8arp.1

Crystal structure of DEAD-box protein Dbp2 in complex with ADP

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.05 Å

Oligo State

homo-hexamer

Ligands

6 x ADP: ADENOSINE-5'-DIPHOSPHATE(Covalent)(Non-covalent)

ADP.1: 16 residues within 4Å: Chain A: F.115, F.133, P.136, Q.140, A.158, T.159, G.160, S.161, G.162, K.163, T.164, L.165, E.205, E.268, R.422 Ligands: MG.3 14 PLIP interactions: 14 interactions with chain A Hydrogen bonds: A:D.134, A:Q.140, A:Q.140, A:G.160, A:G.160, A:K.163, A:T.164, A:T.164, A:E.205 Salt bridges: A:K.163, A:R.422, A:R.422 pi-Stacking: A:F.133, A:F.133 ADP.4: 16 residues within 4Å: Chain B: F.115, E.131, F.133, P.136, Q.140, A.158, T.159, G.160, S.161, G.162, K.163, T.164, L.165, Q.201, E.205, K.208 10 PLIP interactions: 10 interactions with chain B Hydrogen bonds: B:Q.140, B:Q.140, B:S.161, B:S.161, B:K.163, B:T.164, B:T.164, B:Q.201, B:K.208, B:K.208 ADP.6: 12 residues within 4Å: Chain C: F.115, F.133, T.159, S.161, G.162, K.163, T.164, L.165, D.267, E.268, R.422 Ligands: MG.8 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:K.163, C:T.164, C:R.422 Salt bridges: C:K.163 ADP.9: 14 residues within 4Å: Chain D: F.115, F.133, D.134, P.136, Q.140, T.159, G.160, S.161, G.162, K.163, T.164, L.165, E.205, R.422 15 PLIP interactions: 15 interactions with chain D Hydrogen bonds: D:D.134, D:Q.140, D:S.161, D:K.163, D:T.164, D:T.164, D:E.268, D:E.268, D:R.422 Salt bridges: D:K.163, D:K.163, D:R.422, D:R.422 pi-Stacking: D:F.133, D:F.133 ADP.11: 13 residues within 4Å: Chain E: F.133, P.136, Q.140, T.159, G.160, S.161, G.162, K.163, T.164, Q.201, E.205, E.268 Ligands: MG.15 14 PLIP interactions: 14 interactions with chain E Hydrogen bonds: E:D.134, E:Q.140, E:Q.140, E:T.159, E:S.161, E:K.163, E:T.164, E:T.164, E:Q.201, E:E.268 Salt bridges: E:K.163, E:K.163 pi-Stacking: E:F.133, E:F.133 ADP.16: 18 residues within 4Å: Chain F: F.115, F.133, D.134, K.135, P.136, T.137, Q.140, A.158, T.159, G.160, S.161, G.162, K.163, T.164, Q.201, E.205, K.208, E.268 17 PLIP interactions: 17 interactions with chain F Hydrogen bonds: F:T.137, F:Q.140, F:Q.140, F:G.160, F:S.161, F:K.163, F:T.164, F:T.164, F:T.164, F:Q.201, F:K.208, F:K.208, F:E.268, F:E.268 Salt bridges: F:K.163 pi-Stacking: F:F.133, F:F.133

8 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 2 residues within 4Å: Chain A: R.381 Chain F: E.382 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.381 SO4.5: 2 residues within 4Å: Chain B: R.381 Chain D: E.382 1 PLIP interactions: 1 interactions with chain B Salt bridges: B:R.381 SO4.7: 2 residues within 4Å: Chain C: R.381 Chain E: E.382 1 PLIP interactions: 1 interactions with chain C Salt bridges: C:R.381 SO4.10: 2 residues within 4Å: Chain B: E.382 Chain D: R.381 1 PLIP interactions: 1 interactions with chain D Salt bridges: D:R.381 SO4.12: 3 residues within 4Å: Chain E: T.377, K.378, R.381 2 PLIP interactions: 2 interactions with chain E Salt bridges: E:K.378, E:R.381 SO4.13: 4 residues within 4Å: Chain E: G.222, T.243, G.245, R.246 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:G.222, E:T.243, E:G.245, E:R.246 SO4.14: 2 residues within 4Å: Chain E: P.225, K.226 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:K.226 Salt bridges: E:K.226 SO4.17: 3 residues within 4Å: Chain A: E.382 Chain F: R.381, K.394 2 PLIP interactions: 2 interactions with chain F Salt bridges: F:R.381, F:K.394

3 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 4 residues within 4Å: Chain A: T.164, D.267, E.268 Ligands: ADP.1 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:T.164, A:D.267 MG.8: 4 residues within 4Å: Chain C: K.163, D.267, E.268 Ligands: ADP.6 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:E.268 MG.15: 4 residues within 4Å: Chain E: K.163, T.164, D.267 Ligands: ADP.11 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:D.267

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Song, Q.X. et al., Nonstructural N- and C-tails of Dbp2 confer the protein full helicase activities. J.Biol.Chem. (2023)

Release Date

2023-03-22

Peptides

ATP-dependent RNA helicase DBP2: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

ATP-dependent RNA helicase DBP2

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