4X3R
Avi-GCPII structure in complex with FITC-conjugated GCPII-specific inhibitor
- PDB DOI: https://doi.org/10.2210/pdb4X3R/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Drosophila melanogaster
- Mutation(s): No 
- Deposited: 2014-12-01 Released: 2015-10-14 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.86 Å
- R-Value Free: 0.180 
- R-Value Work: 0.148 
- R-Value Observed: 0.149 
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 | 739 | 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, D | 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 | E | 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)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | F | 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 | |
686 Query on 686 | M [auth A] | N-({(1S)-5-[(4-bromobenzyl)({6-[4-(4-{4-[4-carboxy-3-(6-hydroxy-3-oxo-3H-xanthen-9-yl)benzoyl]piperazin-1-yl}phenyl)piperazin-1-yl]pyridin-3-yl}carbonyl)amino]-1-carboxypentyl}carbamoyl)-L-glutamic acid C60 H59 Br N8 O14 HNPUHOJFAXMPAU-GTMCEHENSA-N | |||
NAG Query on NAG | K [auth A], L [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
ZN Query on ZN | G [auth A], H [auth A] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N | |||
CA Query on CA | J [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: 1.86 Å
- R-Value Free: 0.180 
- R-Value Work: 0.148 
- R-Value Observed: 0.149 
- Space Group: I 2 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 101.71 | α = 90 |
b = 130.163 | β = 90 |
c = 159.536 | γ = 90 |
Software Name | Purpose |
---|---|
XSCALE | data scaling |
MOLREP | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
XDS | data reduction |
Entry History 
Deposition Data
- Released Date: 2015-10-14  Deposition Author(s): Tykvart, J., Konvalinka, J.
Revision History (Full details and data files)
- Version 1.0: 2015-10-14
Type: Initial release - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-01-10
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary