Download MendeleyStructural basis for inhibition mechanism of human cytosolic beta-glucosidase by monnoside
Noguchi, J., Hayashi, Y., Okino, N., Ito, M., Kimura, M., Kakuta, Y.To be published.
3VKK
Crystal Structure Of The Covalent Intermediate Of Human Cytosolic Beta-Glucosidase-mannose complex
- PDB DOI: https://doi.org/10.2210/pdb3VKK/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2011-11-17 Released: 2012-11-21
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.222
- R-Value Work: 0.182
- R-Value Observed: 0.184
This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Cytosolic beta-glucosidase | 469 | Homo sapiens | Mutation(s): 1 Gene Names: GBA3, CBG, CBGL1 EC: 3.2.1.21 (PDB Primary Data), 3.2.1.46 (UniProt), 3.2.1.45 (UniProt) |  | |
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for Q9H227 (Homo sapiens) Explore Q9H227 Go to UniProtKB: Q9H227 | |||||
PHAROS: Q9H227 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9H227 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 6 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| OLA Query on OLA | G [auth A] | OLEIC ACID C18 H34 O2 ZQPPMHVWECSIRJ-KTKRTIGZSA-N |  | ||
| PLM Query on PLM | F [auth A] | PALMITIC ACID C16 H32 O2 IPCSVZSSVZVIGE-UHFFFAOYSA-N |  | ||
| MAN Query on MAN | I [auth A] | alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N |  | ||
| GOL Query on GOL | B [auth A], D [auth A], H [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| CL Query on CL | C [auth A], E [auth A] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| MG Query on MG | J [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.222
- R-Value Work: 0.182
- R-Value Observed: 0.184
- Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 65.733 | α = 90 |
| b = 83.519 | β = 90 |
| c = 90.892 | γ = 90 |
| Software Name | Purpose |
|---|---|
| ADSC | data collection |
| MOLREP | phasing |
| REFMAC | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2012-11-21 Deposition Author(s): Noguchi, J., Hayashi, Y., Okino, N., Ito, M., Kimura, M., Kakuta, Y.
Revision History (Full details and data files)
- Version 1.0: 2012-11-21
Type: Initial release - Version 1.1: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Database references, Derived calculations, Structure summary - Version 1.2: 2024-11-06
Changes: Data collection, Database references, Structure summary
