SMTL ID : 7pmq.1 (1 other biounit)

DEAD-box helicase DbpA in the active conformation bound to a hairpin loop RNA and ADP/BeF3

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.22 Å

Oligo State

homo-dimer

Ligands

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

ADP.1: 20 residues within 4Å: Chain A: F.6, G.24, Y.25, T.27, T.29, Q.32, K.50, G.52, S.53, G.54, K.55, T.56, E.92, G.306, D.308, K.310, R.336, A.337 Ligands: BEF.2, MG.3 18 PLIP interactions: 18 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, A:K.310 Salt bridges: A:K.55, A:R.336, A:R.336 pi-Stacking: A:Y.25, A:Y.25 ADP.4: 17 residues within 4Å: Chain B: Y.25, T.27, T.29, Q.32, K.50, 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 15 PLIP interactions: 15 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:E.92, B:D.308 Salt bridges: B:K.55, B:R.336, B:R.336 pi-Stacking: B:Y.25, B:Y.25

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

BEF.2: 8 residues within 4Å: Chain A: T.51, K.55, E.156, G.306, R.333, R.336 Ligands: ADP.1, MG.3 No protein-ligand interaction detected (PLIP) BEF.5: 7 residues within 4Å: Chain B: 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 B: T.56, D.155, E.156 Ligands: ADP.4, BEF.5 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.155

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

PO4.7: 2 residues within 4Å: Chain A: P.113 Chain C: G.1 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:G.115 PO4.8: 1 residues within 4Å: Chain D: G.1 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
C

B
D

ATP-dependent RNA helicase DbpA

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