1Y7V

X-ray structure of human acid-beta-glucosidase covalently bound to conduritol B epoxide

Structural Biology Knowledgebase: 1Y7V SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.242

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1Y7V

Classification: HYDROLASE

Total Structure Weight: 113739.67

Macromolecule Entities
Molecule Chains Length Organism Details
Glucosylceramidase A, B 497 Homo sapiens EC#: 3.2.1.45 IUBMB
Mutation: R495H
Gene Name(s): GBA Gene View GC Gene View GLUC

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
INS
Query on INS

A, B 1,2,3,4,5,6-HEXAHYDROXY-CYCLOHEXANE
MYO-INOSITOL (Synonym)
C6 H12 O6
CDAISMWEOUEBRE-GPIVLXJGSA-N
Ligand Explorer
 
JSmol
NAG
Query on NAG

A, B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
JSmol
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
JSmol

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.280
  • R-Value Work: 0.242
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 104.49 α = 90.00
b = 285.61 β = 90.00
c = 91.51 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-12-10
  • 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

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4