4Y63

AAGlyB in complex with amino-acid analogues


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history


Literature

Design of Glycosyltransferase Inhibitors: Serine Analogues as Pyrophosphate Surrogates?

Wang, S.Cuesta-Seijo, J.A.Striebeck, A.Lafont, D.Palcic, M.M.Vidal, S.

(2015) Chempluschem 80: 1525-1532


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Histo-blood group ABO system transferase354Homo sapiensMutation(s): 1 
Gene Names: ABO
EC: 2.4.1.40 (PDB Primary Data), 2.4.1.37 (PDB Primary Data)
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 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
BHE
Query on BHE

Download Ideal Coordinates CCD File 
B [auth A]octyl 2-O-(6-deoxy-alpha-L-galactopyranosyl)-beta-D-galactopyranoside
C20 H38 O10
GTTDTLMUWQMDNA-ARNYJBIMSA-N
48O
Query on 48O

Download Ideal Coordinates CCD File 
C [auth A]5'-deoxy-5'-{[(2S)-2-(triaza-1,2-dien-2-ium-1-yl)propanoyl]amino}uridine
C12 H17 N6 O6
BMVPLHCMGOWMGY-DANLAGSESA-O
MN
Query on MN

Download Ideal Coordinates CCD File 
D [auth A]MANGANESE (II) ION
Mn
WAEMQWOKJMHJLA-UHFFFAOYSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.30 Å
  • R-Value Free: 0.183 
  • R-Value Work: 0.159 
  • R-Value Observed: 0.160 
  • Space Group: C 2 2 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.84α = 90
b = 149.15β = 90
c = 80.09γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing

Structure Validation

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-09-16
    Type: Initial release
  • Version 1.1: 2017-08-30
    Changes: Database references
  • Version 1.2: 2024-01-10
    Changes: Data collection, Database references, Refinement description