2NSX

Structure of acid-beta-glucosidase with pharmacological chaperone provides insight into Gaucher disease

PDB DOI: https://doi.org/10.2210/pdb2NSX/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): No

Deposited: 2006-11-06 Released: 2006-12-26
Deposition Author(s): Lieberman, R.L., Petsko, G.A., Ringe, D.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.235
R-Value Work: 0.191
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 225.87 kDa
Atom Count: 16,918
Modelled Residue Count: 1,988
Deposited Residue Count: 1,988
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glucosylceramidase	A, B, C, D	497	Homo sapiens	Mutation(s): 0 Gene Names: GBA EC: 3.2.1.45
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
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain U [auth C] SDF format, chain Z [auth D] MOL2 format, chain E [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain U [auth C] MOL2 format, chain Z [auth D]	E [auth A], L [auth B], M [auth B], U [auth C], Z [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain U [auth C] Focus chain Z [auth D] Interactions & Density Focus chain E [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain U [auth C] Focus chain Z [auth D]
IFM Query on IFM Download Ideal Coordinates CCD File SDF format, chain EA [auth D] SDF format, chain T [auth B] MOL2 format, chain EA [auth D] MOL2 format, chain T [auth B]	EA [auth D], T [auth B]	5-HYDROXYMETHYL-3,4-DIHYDROXYPIPERIDINE C₆ H₁₃ N O₃ QPYJXFZUIJOGNX-HSUXUTPPSA-N		Interactions Focus chain EA [auth D] Focus chain T [auth B] Interactions & Density Focus chain EA [auth D] Focus chain T [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain BA [auth D] SDF format, chain CA [auth D] SDF format, chain DA [auth D] SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain J [auth A] SDF format, chain N [auth B] 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 V [auth C] SDF format, chain W [auth C] SDF format, chain X [auth C] SDF format, chain AA [auth D] SDF format, chain G [auth A] SDF format, chain I [auth A] SDF format, chain S [auth B] MOL2 format, chain BA [auth D] MOL2 format, chain CA [auth D] MOL2 format, chain DA [auth D] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] 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 V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain X [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain G [auth A] MOL2 format, chain I [auth A] MOL2 format, chain S [auth B]	AA [auth D] BA [auth D] CA [auth D] DA [auth D] F [auth A] AA [auth D], BA [auth D], CA [auth D], DA [auth D], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], R [auth B], S [auth B], V [auth C], W [auth C], X [auth C]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] 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 N [auth B] 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] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain CA [auth D] Focus chain DA [auth D] 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 N [auth B] 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] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain K [auth A] MOL2 format, chain Y [auth C] MOL2 format, chain K [auth A]	K [auth A], Y [auth C]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain Y [auth C] Interactions & Density Focus chain K [auth A] Focus chain Y [auth C]

Binding Affinity Annotations
ID	Source	Binding Affinity
IFM	BindingDB: 2NSX	Ki: 1.7 (nM) from 1 assay(s)
	BindingDB: 2NSX	IC50: min: 8.2, max: 3.10e+4 (nM) from 6 assay(s)
	PDBBind: 2NSX	IC50: 63 (nM) from 1 assay(s)
	Binding MOAD: 2NSX	IC50: 59 (nM) from 1 assay(s)
GIF	BindingDB: 2NSX	Ki: min: 5, max: 23 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.11 Å
R-Value Free: 0.235
R-Value Work: 0.191
R-Value Observed: 0.193
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.967	α = 90
b = 92.216	β = 110.94
c = 152.67	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MAR345	data collection
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-12-26

Deposition Author(s):

Lieberman, R.L.

Petsko, G.A.

Ringe, D.

Revision History (Full details and data files)

Version 1.0: 2006-12-26
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2017-10-18
Changes: Refinement description
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Non-polymer description, Structure summary
Version 2.1: 2023-08-30
Changes: Data collection, Database references, Refinement description, Structure summary