5D29

X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a hydroxamate inhibitor JHU241

• PDB DOI: https://doi.org/10.2210/pdb5D29/pdb

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


• Deposited: 2015-08-05 Released: 2016-04-27 
• Deposition Author(s): Barinka, C., Novakova, Z., Pavlicek, J.
• Funding Organization(s): Helmholtz-Zentrum Berlin and BioStruct-X

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.205 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 

Biological Assembly 1  

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 81.37 kDa 
• Atom Count: 6,297 
• Modelled Residue Count: 686 
• Deposited Residue Count: 695 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate carboxypeptidase 2	A	695	Homo sapiens	Mutation(s): 0  Gene Names: FOLH1, FOLH, NAALAD1, PSM, PSMA, GIG27 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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B, C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-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	D	4		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G31886NL GlyCosmos:  G31886NL GlyGen:  G31886NL

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
5Q1	N [auth A]	4-[(2~{S})-2-carboxy-5-(oxidanylamino)-5-oxidanylidene-pentyl]benzoic acid C13 H15 N O6 VUDGMYIWOPKVSL-JTQLQIEISA-N
NAG	E [auth A], F [auth A], G [auth A], H [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
ZN	I [auth A], J [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
ACT	M [auth A]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
CA	K [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	L [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
5Q1	Binding MOAD:  5D29	IC50: 97 (nM) from 1 assay(s)
	BindingDB:  5D29	IC50: 97 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.205 
• R-Value Work: 0.174 
• R-Value Observed: 0.176 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.191	α = 90
b = 130.459	β = 90
c = 157.196	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
XSCALE	data scaling
MAR345dtb	data collection

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2016-04-27 
Deposition Author(s): Barinka, C., Novakova, Z., Pavlicek, J.

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Funding Organization	Location	Grant Number
Helmholtz-Zentrum Berlin and BioStruct-X	Germany	N283570

Revision History  

• Version 1.0: 2016-04-27
  Type: Initial release
  
• Version 1.1: 2016-06-08
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary