SMTL ID : 7pli.1 (2 other biounits)

DEAD-box helicase DbpA bound to single stranded RNA and ADP/BeF3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 19 residues within 4Å: Chain A: F.6, Y.25, T.27, T.29, Q.32, K.50, T.51, G.52, S.53, G.54, K.55, T.56, E.92, D.308, K.310, R.336, A.337 Ligands: BEF.2, MG.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:T.29, A:Q.32, A:Q.32, A:K.50, A:G.52, A:S.53, A:G.54, A:K.55, A:T.56, A:T.56, A:T.56, A:E.92, A:D.308 Water bridges: A:R.336 Salt bridges: A:K.55, A:R.336, A:R.336 ADP.4: 19 residues within 4Å: Chain C: F.6, Y.25, T.27, T.29, Q.32, K.50, T.51, G.52, S.53, G.54, K.55, T.56, E.92, D.308, K.310, R.336, A.337 Ligands: BEF.5, MG.6 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:T.27, C:T.29, C:Q.32, C:K.50, C:G.52, C:S.53, C:G.54, C:K.55, C:T.56, C:T.56, C:T.56, C:E.92, C:D.308 Water bridges: C:K.55, C:K.55, C:R.336, C:R.336 Salt bridges: C:K.55, C:R.336, C:R.336

2 x BEF: BERYLLIUM TRIFLUORIDE ION(Non-covalent)

BEF.2: 9 residues within 4Å: Chain A: T.51, G.52, K.55, E.156, G.306, R.333, R.336 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP) BEF.5: 9 residues within 4Å: Chain C: T.51, G.52, K.55, E.156, G.306, R.333, R.336 Ligands: ADP.4, MG.6 No protein-ligand interaction detected (PLIP)

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 5 residues within 4Å: Chain A: T.56, D.155, E.156 Ligands: ADP.1, BEF.2 No protein-ligand interaction detected (PLIP) MG.6: 5 residues within 4Å: Chain C: T.56, D.155, E.156 Ligands: ADP.4, BEF.5 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wurm, J.P., Structural basis for RNA-duplex unwinding by the DEAD-box helicase DbpA. Rna (2023)

Release Date

2022-09-07

Peptides

ATP-dependent RNA helicase DbpA: AC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
B

ATP-dependent RNA helicase DbpA

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