› 2z0b

X-ray diffraction
2Å resolution

Crystal structure of CBM20 domain of human putative glycerophosphodiester phosphodiesterase 5 (KIAA1434)

Released:
DOI: 10.2210/pdb2z0b/pdb
PDB entry 2z0b coloured by chain, front view.
PDB entry 2z0b coloured by chain, side view.
PDB entry 2z0b coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Saijo S, Nishino A, Kishishita S, Shirouzu M, Yokoyama S, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Function and Biology Details

Reaction catalysed: 
sn-glycero-3-phosphocholine + H(2)O = choline + sn-glycerol 3-phosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assemblies composition:
monomeric (preferred)
homo dimer
Assembly name:
PDBe Complex ID:
PDB-CPX-192473 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Glycerophosphocholine phosphodiesterase GPCPD1 Chains: A, B, C, D, E, F
Molecule details ›
Chains: A, B, C, D, E, F
Length: 131 amino acids
Theoretical weight: 14.06 KDa
Source organism: Homo sapiens
Expression system: Cell-free protein synthesis
UniProt:
  • Canonical: Q9NPB8 (Residues: 3-120; Coverage: 18%)
Gene names: GDE5, GPCPD1, KIAA1434
Sequence domains: Starch binding domain
Structure domains: Immunoglobulins

Ligands and Environments

1 bound ligand:
Ligand PO4 2 x PO4
1 modified residue:
Ligand MSE 6 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B2
Spacegroup: P31
Unit cell:
a: 111.04Å b: 111.04Å c: 77.385Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.222 0.221 0.243
Expression system: Cell-free protein synthesis

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