1Y7V
X-ray structure of human acid-beta-glucosidase covalently bound to conduritol B epoxide
- PDB DOI: https://doi.org/10.2210/pdb1Y7V/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Cricetulus griseus
- Mutation(s): Yes 
- Deposited: 2004-12-10 Released: 2005-04-12 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.280 
- R-Value Work: 0.242 
- R-Value Observed: 0.244 
This is version 2.2 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 |
Glucosylceramidase | 497 | Homo sapiens | Mutation(s): 1  Gene Names: GBA, GC EC: 3.2.1.45 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P04062 (Homo sapiens) Explore P04062  Go to UniProtKB:  P04062 | |||||
PHAROS:  P04062 GTEx:  ENSG00000177628  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P04062 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
INS Query on INS | L [auth A], S [auth B] | 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE C6 H12 O6 CDAISMWEOUEBRE-GPIVLXJGSA-N | |||
SO4 Query on SO4 | E [auth A] F [auth A] G [auth A] H [auth A] I [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.40 Å
- R-Value Free: 0.280 
- R-Value Work: 0.242 
- R-Value Observed: 0.244 
- Space Group: C 2 2 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 104.49 | α = 90 |
b = 285.61 | β = 90 |
c = 91.51 | γ = 90 |
Software Name | Purpose |
---|---|
XDS | data scaling |
XSCALE | data scaling |
CNS | refinement |
XDS | data reduction |
CNS | phasing |
Entry History 
Deposition Data
- Released Date: 2005-04-12  Deposition Author(s): Premkumar, L., Sawkar, A.R., Boldin-Adamsky, S., Toker, L., Silman, I., Kelly, J.W., Futerman, A.H., Sussman, J.L., Israel Structural Proteomics Center (ISPC)
Revision History (Full details and data files)
- Version 1.0: 2005-04-12
Type: Initial release - Version 1.1: 2008-04-30
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2021-10-20
Changes: Database references, Structure summary - Version 2.2: 2023-08-23
Changes: Data collection, Refinement description