3U0X

Crystal structure of the B-specific-1,3-galactosyltransferase (GTB) in complex with compound 382


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

A novel compound from a molecular fragment library screen inhibits glycosyltransferases by displacing the metal ion and interfering with substrate binding

Jorgensen, R.Grimm, L.L.Sindhuwinata, N.Peters, T.Palcic, M.M.

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histo-blood group ABO system transferase
A, B
298Homo sapiensMutation(s): 0 
Gene Names: ABO
EC: 2.4.1.37
UniProt & NIH Common Fund Data Resources
Find proteins for P16442 (Homo sapiens)
Explore P16442 
Go to UniProtKB:  P16442
PHAROS:  P16442
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP16442
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 4 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
GTI
Query on GTI

Download Ideal Coordinates CCD File 
C [auth A],
N [auth B]
1-(3-phenyl-1,2,4-thiadiazol-5-yl)piperazine
C12 H14 N4 S
UMFMHSLRNJBGKO-UHFFFAOYSA-N
SO4
Query on SO4

Download Ideal Coordinates CCD File 
J [auth A]
K [auth A]
L [auth A]
M [auth A]
Q [auth B]
J [auth A],
K [auth A],
L [auth A],
M [auth A],
Q [auth B],
R [auth B],
S [auth B]
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
GOL
Query on GOL

Download Ideal Coordinates CCD File 
F [auth A]
G [auth A]
H [auth A]
I [auth A]
O [auth B]
F [auth A],
G [auth A],
H [auth A],
I [auth A],
O [auth B],
P [auth B]
GLYCEROL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL
Query on CL

Download Ideal Coordinates CCD File 
D [auth A],
E [auth A]
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.190 
  • R-Value Work: 0.154 
  • R-Value Observed: 0.155 
  • Space Group: C 2 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.15α = 90
b = 151.79β = 90
c = 72.34γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PHASERphasing
PHENIXrefinement
PDB_EXTRACTdata extraction
ADSCdata collection
XDSdata 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: 2012-10-24
    Type: Initial release
  • Version 1.1: 2014-11-12
    Changes: Structure summary
  • Version 1.2: 2023-09-13
    Changes: Data collection, Database references, Derived calculations, Refinement description