2CIJ | pdb_00002cij

membrane-bound glutamate carboxypeptidase II (GCPII) with bound methionine

• PDB DOI: https://doi.org/10.2210/pdb2CIJ/pdb

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


• Deposited: 2006-03-21 Released: 2007-03-27 
• Deposition Author(s): Barinka, C., Plechanovova, A., Rulisek, L., Mlcochova, P., Majer, P., Slusher, B.S., Hilgenfeld, R., Mesters, J.R., Konvalinka, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.219 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.174 (Depositor) 

Starting Model: experimental

Literature

Glutamate Carboxypeptidase II

Mesters, J.R., Hilgenfeld, R.

(2011) Handbook Of Metalloproteins 4: 681

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 PQS (software)

Macromolecule Content 

• Total Structure Weight: 82.66 kDa 
• Atom Count: 5,730 
• 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 II	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	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
NAG	K [auth A], L [auth A], M [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MET	F [auth A]	METHIONINE C5 H11 N O2 S FFEARJCKVFRZRR-BYPYZUCNSA-N
ZN	G [auth A], H [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA	I [auth A]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
CL	J [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.219 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.172 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.174 (Depositor) 

Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.692	α = 90
b = 130.777	β = 90
c = 160.303	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-03-27 
Deposition Author(s): Barinka, C., Plechanovova, A., Rulisek, L., Mlcochova, P., Majer, P., Slusher, B.S., Hilgenfeld, R., Mesters, J.R., Konvalinka, J.

Revision History  

• Version 1.0: 2007-03-27
  Type: Initial release
  
• Version 1.1: 2014-06-11
  Changes: Database references, Derived calculations, Other, Structure summary, Version format compliance
• Version 1.2: 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: 2024-11-13
  Changes: Structure summary