› 2rkb

X-ray diffraction
2.8Å resolution

Serine dehydratase like-1 from human cancer cells

Released:
DOI: 10.2210/pdb2rkb/pdb
PDB entry 2rkb coloured by chain, front view.
PDB entry 2rkb coloured by chain, side view.
PDB entry 2rkb coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
A catalytic mechanism that explains a low catalytic activity of serine dehydratase like-1 from human cancer cells: crystal structure and site-directed mutagenesis studies.
Yamada T, Komoto J, Kasuya T, Takata Y, Ogawa H, Mori H, Takusagawa F
Biochim Biophys Acta 1780 809-18 (2008)
PMID: 18342636

Function and Biology Details

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

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-188515 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Serine dehydratase-like Chains: A, B, C, D, E
Molecule details ›
Chains: A, B, C, D, E
Length: 318 amino acids
Theoretical weight: 33.57 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q96GA7 (Residues: 11-328; Coverage: 97%)
Gene name: SDSL
Sequence domains: Pyridoxal-phosphate dependent enzyme
Structure domains: Rossmann fold

Ligands and Environments


Cofactor: Ligand PLP 5 x PLP
1 bound ligand:
Ligand K 5 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: C2221
Unit cell:
a: 97.21Å b: 154.74Å c: 306.37Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.213 0.213 0.23
Expression system: Escherichia coli

Quick links

Citations

6 citation in other articles

Crystal structure of a homolog of mammalian serine racemase from Schizosaccharomyces pombe.
Goto et al. (2009)
5 more

1 mention without citation

The dipeptidyl peptidase IV inhibitors vildagliptin and K-579 inhibit a phospholipase C: a case of promiscuous scaffolds in proteins.
Chakraborty et al. (2013)