3WEZ

Crystal structure of human beta-galactosidase in complex with NOEV


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 

Starting Model: experimental
View more details

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Structural basis of pharmacological chaperoning for human beta-galactosidase

Suzuki, H.Ohto, U.Higaki, K.Mena-Barragan, T.Aguilar-Moncayo, M.Ortiz Mellet, C.Nanba, E.Garcia Fernandez, J.M.Suzuki, Y.Shimizu, T.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Beta-galactosidase
A, B, C, D
678Homo sapiensMutation(s): 0 
Gene Names: ELNR1GLB1
EC: 3.2.1.23
UniProt & NIH Common Fund Data Resources
Find proteins for P16278 (Homo sapiens)
Explore P16278 
Go to UniProtKB:  P16278
PHAROS:  P16278
GTEx:  ENSG00000170266 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16278
Glycosylation
Glycosylation Sites: 4Go to GlyGen: P16278-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
N8V
Query on N8V

Download Ideal Coordinates CCD File 
DA [auth C],
J [auth A],
NA [auth D],
T [auth B]
(1S,2S,3S,6R)-4-(hydroxymethyl)-6-(octylamino)cyclohex-4-ene-1,2,3-triol
C15 H29 N O4
UPZUHYMBTUUPML-QPSCCSFWSA-N
NAG
Query on NAG

Download Ideal Coordinates CCD File 
AA [auth C]
BA [auth C]
E [auth A]
F [auth A]
G [auth A]
AA [auth C],
BA [auth C],
E [auth A],
F [auth A],
G [auth A],
H [auth A],
IA [auth D],
JA [auth D],
KA [auth D],
LA [auth D],
O [auth B],
P [auth B],
Q [auth B],
R [auth B],
Y [auth C],
Z [auth C]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
EA [auth C]
FA [auth C]
K [auth A]
L [auth A]
OA [auth D]
EA [auth C],
FA [auth C],
K [auth A],
L [auth A],
OA [auth D],
PA [auth D],
U [auth B],
V [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
EDO
Query on EDO

Download Ideal Coordinates CCD File 
GA [auth C]
HA [auth C]
M [auth A]
N [auth A]
QA [auth D]
GA [auth C],
HA [auth C],
M [auth A],
N [auth A],
QA [auth D],
RA [auth D],
W [auth B],
X [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
CA [auth C],
I [auth A],
MA [auth D],
S [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Binding Affinity Annotations 
IDSourceBinding Affinity
N8V BindingDB:  3WEZ Ki: min: 300, max: 510 (nM) from 2 assay(s)
IC50: 125 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.179 
  • R-Value Observed: 0.181 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 94.933α = 90
b = 115.915β = 92.25
c = 140.51γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2014-04-23
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary
  • Version 1.2: 2023-11-08
    Changes: Data collection, Database references, Refinement description, Structure summary