2JBJ

membrane-bound glutamate carboxypeptidase II (GCPII) in complex with 2-PMPA (2-phosphonoMethyl-pentanedioic acid)

• PDB DOI: https://doi.org/10.2210/pdb2JBJ/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: 2.19 Å
• R-Value Free: 0.238 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 

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: 82.73 kDa 
• Atom Count: 5,914 
• Modelled 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

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, D	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D 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
G88	M [auth A]	(2S)-2-(PHOSPHONOMETHYL)PENTANEDIOIC ACID C6 H11 O7 P ISEYJGQFXSTPMQ-SCSAIBSYSA-N
NAG	J [auth A], K [auth A], L [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-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

Binding Affinity Annotations
ID	Source	Binding Affinity
G88	BindingDB:  2JBJ	Ki: min: 0.1, max: 31 (nM) from 8 assay(s)
		Kd: min: 0.4, max: 0.5 (nM) from 2 assay(s)
		IC50: min: 0.1, max: 300 (nM) from 7 assay(s)
		EC50: 0.62 (nM) from 1 assay(s)
	Binding MOAD:  2JBJ	Ki: 0.2 (nM) from 1 assay(s)
	PDBBind:  2JBJ	Ki: 0.2 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.19 Å
• R-Value Free: 0.238 
• R-Value Work: 0.192 
• R-Value Observed: 0.193 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 100.755	α = 90
b = 130.982	β = 90
c = 159.611	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL	data reduction
SCALEPACK	data scaling

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 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary