2NT1

Structure of acid-beta-glucosidase at neutral pH


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Glucosylceramidase
A, B, C, D
497Homo sapiensMutation(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 Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04062
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth B],
E [auth A],
RB [auth D],
TA [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
PO4
Query on PO4

Download Ideal Coordinates CCD File 
AB [auth C]
AC [auth D]
BA [auth B]
BB [auth C]
BC [auth D]
AB [auth C],
AC [auth D],
BA [auth B],
BB [auth C],
BC [auth D],
CA [auth B],
CB [auth C],
CC [auth D],
DA [auth B],
DB [auth C],
DC [auth D],
EA [auth B],
EB [auth C],
EC [auth D],
F [auth A],
FA [auth B],
FB [auth C],
FC [auth D],
G [auth A],
GA [auth B],
GB [auth C],
GC [auth D],
H [auth A],
HA [auth B],
HB [auth C],
HC [auth D],
I [auth A],
IA [auth B],
IB [auth C],
J [auth A],
JA [auth B],
JB [auth C],
K [auth A],
KA [auth B],
KB [auth C],
L [auth A],
LA [auth B],
LB [auth C],
M [auth A],
MA [auth B],
MB [auth C],
N [auth A],
NA [auth B],
NB [auth C],
O [auth A],
OA [auth B],
OB [auth C],
P [auth A],
PA [auth B],
PB [auth C],
Q [auth A],
QA [auth B],
QB [auth C],
R [auth A],
RA [auth B],
S [auth A],
SA [auth B],
SB [auth D],
T [auth A],
TB [auth D],
U [auth A],
UA [auth C],
UB [auth D],
V [auth A],
VA [auth C],
VB [auth D],
W [auth A],
WA [auth C],
WB [auth D],
X [auth A],
XA [auth C],
XB [auth D],
Y [auth A],
YA [auth C],
YB [auth D],
Z [auth A],
ZA [auth C],
ZB [auth D]
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.240 
  • R-Value Work: 0.175 
  • R-Value Observed: 0.178 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 110.185α = 90
b = 91.792β = 110.91
c = 153.036γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
MAR345data collection
HKL-2000data reduction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

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: Derived calculations, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.5: 2023-08-30
    Changes: Data collection, Database references, Refinement description, Structure summary