4JZ0
X-ray structure of human glutamate carboxypeptidase II (GCPII) in complex with CTT1055
- PDB DOI: https://doi.org/10.2210/pdb4JZ0/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Drosophila melanogaster
- Mutation(s): No 
- Deposited: 2013-04-02 Released: 2014-04-02 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.83 Å
- R-Value Free: 0.171 
- R-Value Work: 0.152 
- R-Value Observed: 0.153 
This is version 2.0 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 | 709 | Homo sapiens | Mutation(s): 0  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  | |||||
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, 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 | 3D Interactions | |
T01 Query on T01 | M [auth A] | N-(4-fluorobenzoyl)-L-gamma-glutamyl-O-[(S)-{[(1S)-1,3-dicarboxypropyl]amino}(hydroxy)phosphoryl]-L-serine C20 H25 F N3 O13 P MVGKQICKXWWQHS-IHRRRGAJSA-N | |||
NAG Query on 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 Query on ZN | F [auth A], G [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
CA Query on CA | H [auth A] | CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N | |||
CL Query on CL | I [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.83 Å
- R-Value Free: 0.171 
- R-Value Work: 0.152 
- R-Value Observed: 0.153 
- Space Group: I 2 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 101.819 | α = 90 |
b = 130.399 | β = 90 |
c = 159.987 | γ = 90 |
Software Name | Purpose |
---|---|
SERGUI | data collection |
REFMAC | refinement |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
REFMAC | phasing |
Entry History 
Deposition Data
- Released Date: 2014-04-02  Deposition Author(s): Barinka, C.
Revision History (Full details and data files)
- Version 1.0: 2014-04-02
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary