› 5m5k

X-ray diffraction
1.84Å resolution

S-adenosyl-L-homocysteine hydrolase from Bradyrhizobium elkanii in complex with adenosine and cordycepin

Released:
DOI: 10.2210/pdb5m5k/pdb
PDB entry 5m5k coloured by chain, front view.
PDB entry 5m5k coloured by chain, side view.
PDB entry 5m5k coloured by chain, top view.
Source organism: Bradyrhizobium elkanii
Primary publication:
Crystallographic and SAXS studies of S-adenosyl-l-homocysteine hydrolase from Bradyrhizobium elkanii.
Manszewski T, Szpotkowski K, Jaskolski M
OpenAccess logo IUCrJ 4 271-282 (2017)
PMID: 28512574

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-100662 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Adenosylhomocysteinase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 479 amino acids
Theoretical weight: 52.74 KDa
Source organism: Bradyrhizobium elkanii
Expression system: Escherichia coli
UniProt:
  • Canonical: A0A087WNH6 (Residues: 1-473; Coverage: 100%)
Gene name: ahcY
Sequence domains:
Structure domains:

Ligands and Environments

7 bound ligands:
Ligand NAD 4 x NAD
Ligand ADN 3 x ADN
Ligand NA 3 x NA
Ligand PEG 2 x PEG
Ligand 3AD 1 x 3AD
Ligand PGE 1 x PGE
Ligand ACT 1 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)
Spacegroup: P21212
Unit cell:
a: 108.162Å b: 176.283Å c: 102.349Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.146 0.146 0.192
Expression system: Escherichia coli

Quick links

Citations

3 review citations

Therapeutic Potential and Biological Applications of Cordycepin and Metabolic Mechanisms in Cordycepin-Producing Fungi.
Qin et al. (2019)
2 more

3 mentions without citation

Crystallographic and SAXS studies of S-adenosyl-l-homocysteine hydrolase from Bradyrhizobium elkanii.
Manszewski et al. (2017)
2 more