2JBK | pdb_00002jbk

membrane-bound glutamate carboxypeptidase II (GCPII) in complex with quisqualic acid (quisqualate, alpha-amino-3,5-dioxo-1,2,4- oxadiazolidine-2-propanoic acid)

• PDB DOI: https://doi.org/10.2210/pdb2JBK/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): No 


• Deposited: 2006-12-07 Released: 2006-12-18 
• Deposition Author(s): Mesters, J.R., Henning, K., Hilgenfeld, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Work: 
  0.210 (Depositor) 
• R-Value Observed: 
  0.210 (Depositor) 

Starting Model: experimental

Literature

Human Glutamate Carboxypeptidase II Inhibition: Structures of Gcpii in Complex with Two Potent Inhibitors, Quisqualate and 2-Pmpa.

Mesters, J.R., Henning, K., Hilgenfeld, R.

(2007) Acta Crystallogr D Biol Crystallogr 63: 508

• PubMed: 17372356 
• DOI: https://doi.org/10.1107/S090744490700902X


• PubMed Abstract: 
  

  Human glutamate carboxypeptidase II (GCPII) occurs in the central nervous system as well as in human prostate (where it is called prostate-specific membrane antigen; PSMA). Inhibitors of the enzyme have been shown to provide neuroprotection, but may also be useful for the detection, imaging and treatment of prostate cancer. Crystal structures were determined of the extracellular part of GCPII (amino-acid residues 44-750) in complex with two potent inhibitors, quisqualate and 2-PMPA (the strongest GCPII inhibitor to date), at resolutions of 3.0 and 2.2 A, respectively. In addition, models were constructed for binding of the inhibitors willardiine, homoibotenate, L-2-amino-4-phosphonobutanoic acid and L-serine-O-sulfate to the S1' site of the enzyme. The common denominator for high-affinity binding to the S1' site is the formation of two strong salt bridges.

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Organizational Affiliation: 
• Institute of Biochemistry, Center for Structural and Cell Biology In Medicine, University of Lübeck, Ratzeburger Allee 160, Lübeck 23538, Germany. [e-mail]

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PQS (software)

Macromolecule Content 

• Total Structure Weight: 82.7 kDa 
• Atom Count: 5,532 
• Modeled Residue Count: 687 
• Deposited Residue Count: 707 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GLUTAMATE CARBOXYPEPTIDASE 2	A	707	Homo sapiens	Mutation(s): 0  EC: 3.4.17.21
UniProt & NIH Common Fund Data Resources
Find proteins for Q04609 (Homo sapiens) Explore Q04609  Go to UniProtKB:  Q04609
PHAROS:  Q04609 GTEx:  ENSG00000086205
Glycosylation
Glycosylation Sites: 7		Go to GlyGen: Q04609-1

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C, D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	4		N-Glycosylation
Glycosylation Resources
GlyTouCan: G81315DD GlyCosmos: G81315DD GlyGen: G81315DD

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	J [auth A], K [auth A], L [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
QUS	M [auth A]	(S)-2-AMINO-3-(3,5-DIOXO-[1,2,4]OXADIAZOLIDIN-2-YL)-PROPIONIC ACID C5 H7 N3 O5 ASNFTDCKZKHJSW-REOHCLBHSA-N
ZN	F [auth A], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	H [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	I [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.99 Å
• R-Value Work:  0.210 (Depositor) 
• R-Value Observed: 0.210 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 103.144	α = 90
b = 130.758	β = 90
c = 159.992	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
H	data reduction
SCALEPACK	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-12-18 
Deposition Author(s): Mesters, J.R., Henning, K., Hilgenfeld, R.

Revision History  

• Version 1.0: 2006-12-18
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2019-07-24
  Changes: Data collection, Derived calculations
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
• Version 2.2: 2024-10-23
  Changes: Structure summary