SMTL ID : 7pmm.1

DEAD-box helicase DbpA in the active conformation bound to a ss/dsRNA junction and ADP/BeF3

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 18 residues within 4Å: Chain A: 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 19 PLIP interactions: 19 interactions with chain A Hydrogen bonds: A:T.27, A:T.29, A:Q.32, 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:K.55, A:K.55, A:D.155, A:R.336 Salt bridges: A:K.55, A:R.336, A:R.336 ADP.4: 19 residues within 4Å: Chain B: F.6, G.24, Y.25, T.27, T.29, Q.32, 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 17 PLIP interactions: 17 interactions with chain B Hydrogen bonds: B:T.27, B:Q.32, B:G.52, B:S.53, B:G.54, B:K.55, B:T.56, B:T.56, B:T.56, B:E.92, B:D.308 Water bridges: B:D.155, B:E.156, B:R.336 Salt bridges: B:K.55, B:R.336, B: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: 10 residues within 4Å: Chain B: T.51, G.52, K.55, E.156, A.187, 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: 4 residues within 4Å: Chain B: T.56, D.155 Ligands: ADP.4, BEF.5 No protein-ligand interaction detected (PLIP)

1 x POP: PYROPHOSPHATE 2-(Non-functional Binders)

POP.7: 2 residues within 4Å: Chain C: G.1, G.2 No protein-ligand interaction detected (PLIP)

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.8: 2 residues within 4Å: Chain D: G.1, G.2 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

2022-09-14

Peptides

ATP-dependent RNA helicase DbpA: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

ATP-dependent RNA helicase DbpA

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