› 3d7d

X-ray diffraction
1.69Å resolution

A high resolution crystal structure of human glutamate carboxypeptidase II (GCPII) in a complex with DCFBD, a urea-based inhibitor

Released:
DOI: 10.2210/pdb3d7d/pdb
PDB entry 3d7d coloured by chain, front view.
PDB entry 3d7d coloured by chain, side view.
PDB entry 3d7d coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Interactions between human glutamate carboxypeptidase II and urea-based inhibitors: structural characterization.
Barinka C, Byun Y, Dusich CL, Banerjee SR, Chen Y, Castanares M, Kozikowski AP, Mease RC, Pomper MG, Lubkowski J
J Med Chem 51 7737-43 (2008)
PMID: 19053759

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 (4 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
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 FBD 1 x FBD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-ID
Spacegroup: I222
Unit cell:
a: 101.93Å b: 130.497Å c: 159.187Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.18 0.199
Expression system: Drosophila melanogaster

Quick links

Citations

13 review citations

PET imaging in prostate cancer: focus on prostate-specific membrane antigen.
Mease et al. (2013)
12 more

5 mentions without citation

Toward the Discovery and Development of PSMA Targeted Inhibitors for Nuclear Medicine Applications.
Pastorino et al. (2020)
4 more