› 4oc5

X-ray diffraction
1.7Å resolution

X-ray structure of of human glutamate carboxypeptidase II (GCPII) in a complex with CHIBzL, a urea-based inhibitor N~2~-{[(S)-carboxy(4-hydroxyphenyl)methyl]carbamoyl}-N~6~-(4-iodobenzoyl)-L-lysine

Released:
DOI: 10.2210/pdb4oc5/pdb
PDB entry 4oc5 coloured by chain, front view.
PDB entry 4oc5 coloured by chain, side view.
PDB entry 4oc5 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structural characterization of P1'-diversified urea-based inhibitors of glutamate carboxypeptidase II.
Pavlicek J, Ptacek J, Cerny J, Byun Y, Skultetyova L, Pomper MG, Lubkowski J, Barinka C
Bioorg Med Chem Lett 24 2340-5 (2014)
PMID: 24731280

Function and Biology Details

Reaction catalysed: 
Release of an unsubstituted, C-terminal glutamyl residue, typically from Ac-Asp-Glu or folylpoly-gamma-glutamates.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-170042 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecules (3 distinct):
Glutamate carboxypeptidase 2 Chain: A
Molecule details ›
Chain: A
Length: 709 amino acids
Theoretical weight: 79.86 KDa
Source organism: Homo sapiens
Expression system: Drosophila melanogaster
UniProt:
  • Canonical: Q04609 (Residues: 44-750; Coverage: 94%)
Gene names: FOLH, FOLH1, GIG27, NAALAD1, PSM, PSMA
Sequence domains:
Structure domains:

Ligands and Environments

Carbohydrate polymer : NEW Components: NAG
Carbohydrate polymer
Carbohydrate polymer : NEW Components: NAG, BMA, MAN
Carbohydrate polymer
5 bound ligands:
Ligand NAG 3 x NAG
Ligand ZN 2 x ZN
Ligand CA 1 x CA
Ligand CL 1 x CL
Ligand 2QM 1 x 2QM
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: I222
Unit cell:
a: 101.578Å b: 130.446Å c: 159.066Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.17 0.169 0.204
Expression system: Drosophila melanogaster

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Citations

1 review citation

Enhanced semiempirical QM methods for biomolecular interactions.
Yilmazer et al. (2015)
5 other articles

1 mention without citation

Structural characterization of P1'-diversified urea-based inhibitors of glutamate carboxypeptidase II.
Pavlicek et al. (2014)