6ETY
X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with a inhibitor JHU3371
- PDB DOI: https://doi.org/10.2210/pdb6ETY/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Drosophila melanogaster
- Mutation(s): No 
- Deposited: 2017-10-27 Released: 2018-11-07 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.68 Å
- R-Value Free: 0.178 
- R-Value Work: 0.155 
- R-Value Observed: 0.156 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Glutamate carboxypeptidase 2 | 707 | 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  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q04609 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
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-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | D | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | E | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO |
Small Molecules
Ligands 5 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
BXK (Subject of Investigation/LOI) Query on BXK | M [auth A] | (2~{S})-2-[[(2~{R})-4-methyl-1-oxidanyl-1-oxidanylidene-pentan-2-yl]carbamoyloxy]pentanedioic acid C12 H19 N O8 WQDZXAWSGIQGKR-SFYZADRCSA-N | |||
NAG Query on NAG | F [auth A], G [auth A], H [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
ZN Query on ZN | I [auth A], J [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
CA Query on CA | K [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
CL Query on CL | L [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.68 Å
- R-Value Free: 0.178 
- R-Value Work: 0.155 
- R-Value Observed: 0.156 
- Space Group: I 2 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 101.646 | α = 90 |
b = 130.72 | β = 90 |
c = 158.234 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
Coot | model building |
Entry History 
Deposition Data
- Released Date: 2018-11-07  Deposition Author(s): Barinka, C., Novakova, Z., Motlova, L.
Revision History (Full details and data files)
- Version 1.0: 2018-11-07
Type: Initial release - Version 1.1: 2019-03-27
Changes: Data collection, Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary