› 5x2l

X-ray diffraction
1.81Å resolution

Crystal Structure of Human Serine Racemase

Released:
DOI: 10.2210/pdb5x2l/pdb
PDB entry 5x2l coloured by chain, front view.
PDB entry 5x2l coloured by chain, side view.
PDB entry 5x2l coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Design, synthesis, and evaluation of novel inhibitors for wild-type human serine racemase.
Takahara S, Nakagawa K, Uchiyama T, Yoshida T, Matsumoto K, Kawasumi Y, Mizuguchi M, Obita T, Watanabe Y, Hayakawa D, Gouda H, Mori H, Toyooka N
Bioorg Med Chem Lett 28 441-445 (2018)
PMID: 29277459

Function and Biology Details

Reactions catalysed: 
(1a) L-serine = 2-aminoprop-2-enoate + H(2)O
(1a) D-serine = 2-aminoprop-2-enoate + H(2)O
L-serine = D-serine
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190449 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Serine racemase Chains: A, B
Molecule details ›
Chains: A, B
Length: 348 amino acids
Theoretical weight: 37.67 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9GZT4 (Residues: 1-340; Coverage: 100%)
Gene name: SRR
Sequence domains: Pyridoxal-phosphate dependent enzyme
Structure domains: Rossmann fold

Ligands and Environments


Cofactor: Ligand PLP 2 x PLP
1 bound ligand:
Ligand MG 2 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B1
Spacegroup: P21212
Unit cell:
a: 80.12Å b: 112.59Å c: 88Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.222 0.22 0.258
Expression system: Escherichia coli

Quick links

Citations

2 citation in other articles

Human Serine Racemase Weakly Binds the Third PDZ Domain of PSD-95.
Giaccari et al. (2022)
1 more

4 mentions without citation

The Energy Landscape of Human Serine Racemase.
Raboni et al. (2018)
3 more