4Y63 | pdb_00004y63

AAGlyB in complex with amino-acid analogues

• PDB DOI: https://doi.org/10.2210/pdb4Y63/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2015-02-12 Released: 2015-09-16 
• Deposition Author(s): Wang, S., Cuesta-Seijo, J.A., Striebeck, A., Lafont, D., Palcic, M.M., Vidal, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.30 Å
• R-Value Free: 
  0.183 (Depositor), 0.184 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.160 (DCC) 
• R-Value Observed: 
  0.160 (Depositor) 

Starting Model: experimental

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

• DOI: https://doi.org/10.1002/cplu.201500282

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 41.78 kDa 
• Atom Count: 2,765 
• Modeled Residue Count: 282 
• Deposited Residue Count: 354 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Histo-blood group ABO system transferase	A	354	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
BHE	B [auth A]	octyl 2-O-(6-deoxy-alpha-L-galactopyranosyl)-beta-D-galactopyranoside C20 H38 O10 GTTDTLMUWQMDNA-ARNYJBIMSA-N
48O	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	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 (Depositor), 0.184 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.160 (DCC) 
• R-Value Observed: 0.160 (Depositor) 

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.84	α = 90
b = 149.15	β = 90
c = 80.09	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-16 
Deposition Author(s): Wang, S., Cuesta-Seijo, J.A., Striebeck, A., Lafont, D., Palcic, M.M., Vidal, S.

Revision History  

• 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