3GXI

Crystal structure of acid-beta-glucosidase at pH 5.5

PDB DOI: https://doi.org/10.2210/pdb3GXI/pdb

Classification: HYDROLASE
Organism(s): Homo sapiens
Expression System: Cricetulus griseus
Mutation(s): Yes

Deposited: 2009-04-02 Released: 2009-05-05
Deposition Author(s): Lieberman, R.L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.231
R-Value Work: 0.191
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 229.43 kDa
Atom Count: 17,770
Modelled Residue Count: 1,988
Deposited Residue Count: 1,988
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, C, D	497	Homo sapiens	Mutation(s): 1 Gene Names: GBA, GC, GLUC 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain EB [auth D] SDF format, chain E [auth A] SDF format, chain MA [auth C] SDF format, chain Y [auth B] MOL2 format, chain EB [auth D] MOL2 format, chain E [auth A] MOL2 format, chain MA [auth C] MOL2 format, chain Y [auth B]	E [auth A], EB [auth D], MA [auth C], Y [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain EB [auth D] Focus chain MA [auth C] Focus chain Y [auth B] Interactions & Density Focus chain E [auth A] Focus chain EB [auth D] Focus chain MA [auth C] Focus chain Y [auth B]
PO4 Query on PO4 Download Ideal Coordinates CCD File SDF format, chain CB [auth C] SDF format, chain DA [auth B] SDF format, chain EA [auth B] SDF format, chain F [auth A] SDF format, chain FA [auth B] SDF format, chain G [auth A] SDF format, chain GA [auth B] SDF format, chain H [auth A] SDF format, chain IA [auth B] SDF format, chain IB [auth D] SDF format, chain J [auth A] SDF format, chain JA [auth B] SDF format, chain KA [auth B] SDF format, chain KB [auth D] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain NB [auth D] SDF format, chain QA [auth C] SDF format, chain QB [auth D] SDF format, chain R [auth A] SDF format, chain RA [auth C] SDF format, chain S [auth A] SDF format, chain SB [auth D] SDF format, chain U [auth A] SDF format, chain V [auth A] SDF format, chain W [auth A] SDF format, chain X [auth A] SDF format, chain Z [auth B] SDF format, chain ZA [auth C] SDF format, chain AA [auth B] SDF format, chain AB [auth C] SDF format, chain BA [auth B] SDF format, chain BB [auth C] SDF format, chain CA [auth B] SDF format, chain DB [auth C] SDF format, chain FB [auth D] SDF format, chain GB [auth D] SDF format, chain HA [auth B] SDF format, chain HB [auth D] SDF format, chain I [auth A] SDF format, chain JB [auth D] SDF format, chain K [auth A] SDF format, chain LA [auth B] SDF format, chain LB [auth D] SDF format, chain M [auth A] SDF format, chain MB [auth D] SDF format, chain NA [auth C] SDF format, chain O [auth A] SDF format, chain OA [auth C] SDF format, chain OB [auth D] SDF format, chain P [auth A] SDF format, chain PA [auth C] SDF format, chain PB [auth D] SDF format, chain Q [auth A] SDF format, chain RB [auth D] SDF format, chain SA [auth C] SDF format, chain T [auth A] SDF format, chain TA [auth C] SDF format, chain UA [auth C] SDF format, chain VA [auth C] SDF format, chain WA [auth C] SDF format, chain XA [auth C] SDF format, chain YA [auth C] MOL2 format, chain CB [auth C] MOL2 format, chain DA [auth B] MOL2 format, chain EA [auth B] MOL2 format, chain F [auth A] MOL2 format, chain FA [auth B] MOL2 format, chain G [auth A] MOL2 format, chain GA [auth B] MOL2 format, chain H [auth A] MOL2 format, chain IA [auth B] MOL2 format, chain IB [auth D] MOL2 format, chain J [auth A] MOL2 format, chain JA [auth B] MOL2 format, chain KA [auth B] MOL2 format, chain KB [auth D] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain NB [auth D] MOL2 format, chain QA [auth C] MOL2 format, chain QB [auth D] MOL2 format, chain R [auth A] MOL2 format, chain RA [auth C] MOL2 format, chain S [auth A] MOL2 format, chain SB [auth D] MOL2 format, chain U [auth A] MOL2 format, chain V [auth A] MOL2 format, chain W [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Z [auth B] MOL2 format, chain ZA [auth C] MOL2 format, chain AA [auth B] MOL2 format, chain AB [auth C] MOL2 format, chain BA [auth B] MOL2 format, chain BB [auth C] MOL2 format, chain CA [auth B] MOL2 format, chain DB [auth C] MOL2 format, chain FB [auth D] MOL2 format, chain GB [auth D] MOL2 format, chain HA [auth B] MOL2 format, chain HB [auth D] MOL2 format, chain I [auth A] MOL2 format, chain JB [auth D] MOL2 format, chain K [auth A] MOL2 format, chain LA [auth B] MOL2 format, chain LB [auth D] MOL2 format, chain M [auth A] MOL2 format, chain MB [auth D] MOL2 format, chain NA [auth C] MOL2 format, chain O [auth A] MOL2 format, chain OA [auth C] MOL2 format, chain OB [auth D] MOL2 format, chain P [auth A] MOL2 format, chain PA [auth C] MOL2 format, chain PB [auth D] MOL2 format, chain Q [auth A] MOL2 format, chain RB [auth D] MOL2 format, chain SA [auth C] MOL2 format, chain T [auth A] MOL2 format, chain TA [auth C] MOL2 format, chain UA [auth C] MOL2 format, chain VA [auth C] MOL2 format, chain WA [auth C] MOL2 format, chain XA [auth C] MOL2 format, chain YA [auth C]	AA [auth B] AB [auth C] BA [auth B] BB [auth C] CA [auth B] AA [auth B], AB [auth C], BA [auth B], BB [auth C], CA [auth B], CB [auth C], DA [auth B], DB [auth C], EA [auth B], F [auth A], FA [auth B], FB [auth D], G [auth A], GA [auth B], GB [auth D], H [auth A], HA [auth B], HB [auth D], I [auth A], IA [auth B], IB [auth D], J [auth A], JA [auth B], JB [auth D], K [auth A], KA [auth B], KB [auth D], L [auth A], LA [auth B], LB [auth D], M [auth A], MB [auth D], N [auth A], NA [auth C], NB [auth D], O [auth A], OA [auth C], OB [auth D], P [auth A], PA [auth C], PB [auth D], Q [auth A], QA [auth C], QB [auth D], R [auth A], RA [auth C], RB [auth D], S [auth A], SA [auth C], SB [auth D], T [auth A], TA [auth C], U [auth A], UA [auth C], V [auth A], VA [auth C], W [auth A], WA [auth C], X [auth A], XA [auth C], YA [auth C], Z [auth B], ZA [auth C]	PHOSPHATE ION O₄ P NBIIXXVUZAFLBC-UHFFFAOYSA-K		Interactions Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth D] Focus chain M [auth A] Focus chain MB [auth D] Focus chain N [auth A] Focus chain NA [auth C] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OA [auth C] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PA [auth C] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RA [auth C] Focus chain RB [auth D] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SB [auth D] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C] Interactions & Density Focus chain AA [auth B] Focus chain AB [auth C] Focus chain BA [auth B] Focus chain BB [auth C] Focus chain CA [auth B] Focus chain CB [auth C] Focus chain DA [auth B] Focus chain DB [auth C] Focus chain EA [auth B] Focus chain F [auth A] Focus chain FA [auth B] Focus chain FB [auth D] Focus chain G [auth A] Focus chain GA [auth B] Focus chain GB [auth D] Focus chain H [auth A] Focus chain HA [auth B] Focus chain HB [auth D] Focus chain I [auth A] Focus chain IA [auth B] Focus chain IB [auth D] Focus chain J [auth A] Focus chain JA [auth B] Focus chain JB [auth D] Focus chain K [auth A] Focus chain KA [auth B] Focus chain KB [auth D] Focus chain L [auth A] Focus chain LA [auth B] Focus chain LB [auth D] Focus chain M [auth A] Focus chain MB [auth D] Focus chain N [auth A] Focus chain NA [auth C] Focus chain NB [auth D] Focus chain O [auth A] Focus chain OA [auth C] Focus chain OB [auth D] Focus chain P [auth A] Focus chain PA [auth C] Focus chain PB [auth D] Focus chain Q [auth A] Focus chain QA [auth C] Focus chain QB [auth D] Focus chain R [auth A] Focus chain RA [auth C] Focus chain RB [auth D] Focus chain S [auth A] Focus chain SA [auth C] Focus chain SB [auth D] Focus chain T [auth A] Focus chain TA [auth C] Focus chain U [auth A] Focus chain UA [auth C] Focus chain V [auth A] Focus chain VA [auth C] Focus chain W [auth A] Focus chain WA [auth C] Focus chain X [auth A] Focus chain XA [auth C] Focus chain YA [auth C] Focus chain Z [auth B] Focus chain ZA [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.231
R-Value Work: 0.191
R-Value Observed: 0.193
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 110.05	α = 90
b = 91.713	β = 111.13
c = 152.283	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2009-05-05

Deposition Author(s):

Lieberman, R.L.

Revision History (Full details and data files)

Version 1.0: 2009-05-05
Type: Initial release
Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary