2VT0

X-ray structure of a conjugate with conduritol-beta-epoxide of acid-beta-glucosidase overexpressed in cultured plant cells

Structural Biology Knowledgebase: 2VT0 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.201
  • R-Value Work: 0.152

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2VT0

Classification: HYDROLASE

Total Structure Weight: 115804.14

Macromolecule Entities
Molecule Chains Length Organism Details
GLUCOSYLCERAMIDASE A, B 505 Homo sapiens EC#: 3.2.1.45 IUBMB
Fragment: TIM BARREL GLUCOSIDASE, RESIDUES 40-536
Mutation: T55P, R495H
Details: THE ENZYME IS COVALENTLY INHIBITED BY CBE
Gene Name(s): GBA Gene View GC Gene View GLUC

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NAG
Query on NAG

A, B N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CBU
Query on CBU

A, B (1R,2R,3S,4S,5S,6S)-CYCLOHEXANE-1,2,3,4,5,6- HEXOL
C6 H12 O6
CDAISMWEOUEBRE-LKPKBOIGSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUC
Query on FUC

A, B ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.15 Å
  • R-Value Free: 0.201
  • R-Value Work: 0.152
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 68.18 α = 90.00
b = 96.88 β = 103.73
c = 83.17 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2008-05-03
  • Released Date: 2008-09-23
  • Deposition author(s): Brumshtein, B., Greenblatt, H.M., Shaaltiel, Y., Aviezer, D., Silman, I., Futerman, A.H., Sussman, J.L.

Revision History

  • 2012-10-10
    Type: Citation | Details: JRNL
  • 2012-10-10
    Type: Biological assembly | Details: REMARK 300,REMARK 350
  • 2012-10-10
    Type: Geometry validation | Details: REMARK 500
  • 2012-10-10
    Type: Version format compliance | Details: REMARK 4
  • 2012-10-10
    Type: Non-polymer description | Details: FORMUL
  • 2012-10-10
    Type: Other | Details: REMARK 525
  • 2012-10-10
    Type: Binding sites and description | Details: REMARK 800,SITE