3WF2

Crystal structure of human beta-galactosidase in complex with NBT-DGJ


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 1.1 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
MoleculeChainsSequence LengthOrganismDetailsImage
Beta-galactosidaseA, B, C, D678Homo 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
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16278
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDJ
Query on NDJ

Download Ideal Coordinates CCD File 
CA [auth C],
J [auth A],
PA [auth D],
T [auth B]
(2R,3S,4R,5S)-N-butyl-3,4,5-trihydroxy-2-(hydroxymethyl)piperidine-1-carbothioamide
C11 H22 N2 O4 S
VCRXDLDGTLMSHK-XFWSIPNHSA-N
 Ligand Interaction
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],
KA [auth D],
LA [auth D],
MA [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
 Ligand Interaction
SO4
Query on SO4

Download Ideal Coordinates CCD File 
DA [auth C],
EA [auth C],
K [auth A],
L [auth A],
QA [auth D],
DA [auth C],
EA [auth C],
K [auth A],
L [auth A],
QA [auth D],
RA [auth D],
U [auth B],
V [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
EDO
Query on EDO

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

Download Ideal Coordinates CCD File 
FA [auth C],
I [auth A],
JA [auth D],
S [auth B]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
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 = 95.119α = 90
b = 116.26β = 92.41
c = 141.768γ = 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: 2014-04-16
    Type: Initial release
  • Version 1.1: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Data collection, Database references, Derived calculations, Structure summary