3KE0 | pdb_00003ke0

Crystal structure of N370S Glucocerebrosidase at acidic pH.

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 
    0.229 (Depositor), 0.226 (DCC) 
  • R-Value Work: 
    0.172 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 
    0.175 (Depositor) 

Starting Model: experimental
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This is version 2.3 of the entry. See complete history. 

Literature

Crystal Structure of Glucocerebrosidase Containing the N370S Mutation, Implications for Chaperon Therapy

Wei, R.R., Boucher, S., Hughes, H., Guziewica, N., Pan, C.Q., Edmunds, T.

To be published.

Macromolecule Content 

  • Total Structure Weight: 113.86 kDa 
  • Atom Count: 8,262 
  • Modeled Residue Count: 994 
  • Deposited Residue Count: 994 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glucosylceramidase
A, B
497Homo sapiensMutation(s): 1 
Gene Names: GBA, GC, GLUC
EC: 3.2.1.45 (PDB Primary Data), 3.2.1.46 (UniProt), 2.4.1 (UniProt), 3.2.1 (UniProt)
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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04062
Glycosylation
Glycosylation Sites: 2
Go to GlyGen: P04062-1
Sequence Annotations
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Reference Sequence

Oligosaccharides

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Entity ID: 2
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose
C
2N/A
Glycosylation Resources
GlyTouCan: G05026ZL
GlyCosmos: G05026ZL
GlyGen: G05026ZL
Entity ID: 3
MoleculeChains Length2D Diagram GlycosylationD Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
D
2N-Glycosylation
Glycosylation Resources
GlyTouCan: G42666HT
GlyCosmos: G42666HT
GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG

Query on NAG


Download:Ideal Coordinates CCD File
T [auth B]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4

Query on SO4


Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
S [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL

Query on GOL


Download:Ideal Coordinates CCD File
M [auth A],
N [auth A],
U [auth B]		GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free:  0.229 (Depositor), 0.226 (DCC) 
  • R-Value Work:  0.172 (Depositor), 0.171 (DCC) 
  • R-Value Observed: 0.175 (Depositor) 
Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 109.465α = 90
b = 285.064β = 90
c = 92.225γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-10-27
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
  • Version 2.1: 2021-10-13
    Changes: Database references, Structure summary
  • Version 2.2: 2023-09-06
    Changes: Data collection, Refinement description
  • Version 2.3: 2024-11-27
    Changes: Structure summary