3SJG

Human glutamate carboxypeptidase II (E424A inactive mutant ) in complex with N-acetyl-aspartyl-aminooctanoic acid

• PDB DOI: https://doi.org/10.2210/pdb3SJG/pdb

• Classification: Hydrolase/hydrolase inhibitor
• Organism(s): Homo sapiens
• Expression System: Drosophila melanogaster
• Mutation(s): Yes 


• Deposited: 2011-06-21 Released: 2011-10-05 
• Deposition Author(s): Plechanovova, A., Byun, Y., Alquicer, G., Skultetyova, L., Mlcochova, P., Nemcova, A., Kim, H., Navratil, M., Mease, R., Lubkowski, J., Pomper, M., Konvalinka, J., Rulisek, L., Barinka, C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.183 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 

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: 83.02 kDa 
• Atom Count: 6,546 
• Modelled Residue Count: 696 
• Deposited Residue Count: 709 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate carboxypeptidase 2	A	709	Homo sapiens	Mutation(s): 1  Gene Names: FOLH, FOLH1, GIG27, NAALAD1, PSM, PSMA 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
SDR	M [auth A]	(2S)-2-[(N-acetyl-L-alpha-aspartyl)amino]nonanoic acid C15 H26 N2 O6 IRKQLRPKWIMPEM-RYUDHWBXSA-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

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 8
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000797 (SDR)	M [auth A]	(2S)-2-[(N-ACETYL-L-ALPHA-ASPARTYL)AMINO]NONANOIC ACID	Polypeptide / Enzyme inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.183 
• R-Value Work: 0.166 
• R-Value Observed: 0.167 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.266	α = 90
b = 129.993	β = 90
c = 159.121	γ = 90

Software Package:

Software Name	Purpose
SERGUI	data collection
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-10-05 
Deposition Author(s): Plechanovova, A., Byun, Y., Alquicer, G., Skultetyova, L., Mlcochova, P., Nemcova, A., Kim, H., Navratil, M., Mease, R., Lubkowski, J., Pomper, M., Konvalinka, J., Rulisek, L., Barinka, C.

Revision History  

• Version 1.0: 2011-10-05
  Type: Initial release
  
• Version 1.1: 2011-11-16
  Changes: Database references
• Version 1.2: 2012-12-12
  Changes: Other
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary