› 8arp

X-ray diffraction
3.05Å resolution

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

Released:
DOI: 10.2210/pdb8arp/pdb
PDB entry 8arp coloured by chain, front view.
PDB entry 8arp coloured by chain, side view.
PDB entry 8arp coloured by chain, top view.
Source organism: Saccharomyces cerevisiae
Primary publication:
Nonstructural N- and C-tails of Dbp2 confer the protein full helicase activities.
Song QX, Liu NN, Liu ZX, Zhang YZ, Rety S, Hou XM, Xi XG
J Biol Chem 104592 (2023)
PMID: 36894019

Function and Biology Details

Reaction catalysed: 
ATP + H(2)O = ADP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo hexamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-216323 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
ATP-dependent RNA helicase DBP2 Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 546 amino acids
Theoretical weight: 61.08 KDa
Source organism: Saccharomyces cerevisiae
Expression system: Escherichia coli K-12
UniProt:
  • Canonical: P24783 (Residues: 1-546; Coverage: 100%)
Gene names: DBP2, N1945, YNL112W
Sequence domains:

Ligands and Environments

3 bound ligands:
Ligand ADP 6 x ADP
Ligand SO4 8 x SO4
Ligand MG 3 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17B1
Spacegroup: P212121
Unit cell:
a: 145.939Å b: 168.843Å c: 168.87Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.654 0.223 0.27
Expression system: Escherichia coli K-12

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Citations

1 review citation

Drug targets regulate systemic metabolism and provide new horizons to treat nonalcoholic steatohepatitis.
Wang et al. (2024)

1 mention without citation

Nonstructural N- and C-tails of Dbp2 confer the protein full helicase activities.
Song et al. (2023)