2WCG

X-ray structure of acid-beta-glucosidase with N-octyl(cyclic guanidine)-nojirimycin in the active site


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.138 

wwPDB Validation 3D Report Full Report



Literature

6-Amino-6-Deoxy-5,6-Di-N-(N'-Octyliminomethylidene)Nojirimycin: Synthesis, Biological Evaluation, and Crystal Structure in Complex with Acid Beta-Glucosidase.

Brumshtein, B.Aguilar-Moncayo, M.Garcia-Moreno, M.I.Ortiz Mellet, C.Garcia Fernandez, J.M.Silman, I.Shaaltiel, Y.Aviezer, D.Sussman, J.L.Futerman, A.H.

(2009) Chembiochem 10: 1480


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
GLUCOSYLCERAMIDASEAB505Homo sapiensMutation(s): 0 
Gene Names: GBAGCGLUC
EC: 3.2.1.45 (PDB Primary Data), 2.4.1 (UniProt), 3.2.1.104 (UniProt)
Find proteins for P04062 (Homo sapiens)
Explore P04062 
Go to UniProtKB:  P04062
NIH Common Fund Data Resources
PHAROS  P04062
Protein Feature View
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  • Reference Sequence
Oligosaccharides

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Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
C, D
3 N-Glycosylation
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
MT5
Query on MT5

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A, B
N-[(3E,5R,6R,7S,8R,8AR)-5,6,7,8-TETRAHYDROXYHEXAHYDROIMIDAZO[1,5-A]PYRIDIN-3(2H)-YLIDENE]OCTAN-1-AMINIUM
C15 H30 N3 O4
DGGJYTDCPYQDLL-RKQHYHRCSA-O
 Ligand Interaction
FUC
Query on FUC

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A, B
alpha-L-fucopyranose
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
 Ligand Interaction
SO4
Query on SO4

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A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
MT5IC50:  4000   nM  Binding MOAD
MT5Ki :  420   nM  PDBBind
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.194 
  • R-Value Work: 0.135 
  • R-Value Observed: 0.138 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 68.311α = 90
b = 96.827β = 104.34
c = 83.234γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-24
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2017-11-15
    Changes: Advisory, Atomic model, Derived calculations, Non-polymer description, Structure summary
  • Version 3.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Other, Structure summary