3KE0

Crystal structure of N370S Glucocerebrosidase at acidic pH.

PDB DOI: https://doi.org/10.2210/pdb3KE0/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): Yes

Deposited: 2009-10-23 Released: 2010-10-27
Deposition Author(s): Wei, R.R., Boucher, S., Pan, C.Q., Edmunds, T.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.229
R-Value Work: 0.172
R-Value Observed: 0.175

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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
Modelled Residue Count: 994
Deposited Residue Count: 994
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosylceramidase	A, B	497	Homo sapiens	Mutation(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 Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04062
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B	Go to GlyGen: P04062-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose	C	2		N/A	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G05026ZL GlyCosmos: G05026ZL GlyGen: G05026ZL

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D	2		N-Glycosylation	Interactions Focus chain D Interactions & Density Focus chain D
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain T [auth B] MOL2 format, chain T [auth B] mmCIF format, chain T [auth B]	T [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain T [auth B] Interactions & Density Focus chain T [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	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		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain U [auth B] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain U [auth B] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain U [auth B]	M [auth A], N [auth A], U [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain U [auth B] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain U [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.70 Å
R-Value Free: 0.229
R-Value Work: 0.172
R-Value Observed: 0.175
Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 109.465	α = 90
b = 285.064	β = 90
c = 92.225	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2010-10-27

Deposition Author(s):

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

Prepare Data

Validate Data

Deposit Data

Help and Resources

3KE0

Crystal structure of N370S Glucocerebrosidase at acidic pH.

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources