2WTX

Insight into the mechanism of enzymatic glycosyltransfer with retention through the synthesis and analysis of bisubstrate glycomimetics of trehalose-6-phosphate synthase

• PDB DOI: https://doi.org/10.2210/pdb2WTX/pdb

• Classification: TRANSFERASE
• Organism(s): Escherichia coli K-12
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-25 Released: 2010-02-23 
• Deposition Author(s): Errey, J.C., Lee, S.S., Gibson, R.P., Martinez-Fleites, C., Barry, C.S., Jung, P.M.J., OSullivan, A., Davis, B.G., Davies, G.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.235 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 

Starting Model: experimental

Literature

Mechanistic Insight Into Enzymatic Glycosyl Transfer with Retention of Configuration Through Analysis of Glycomimetic Inhibitors.

Errey, J.C., Lee, S.S., Gibson, R.P., Martinez Fleites, C., Barry, C.S., Jung, P.M.J., O'Sullivan, A.C., Davis, B.G., Davies, G.J.

(2010) Angew Chem Int Ed Engl 49: 1234

• PubMed: 20077550 
• DOI: https://doi.org/10.1002/anie.200905096
• Primary Citation of Related Structures:  
  2WTX

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Organizational Affiliation: 

Department of Chemistry, University of Oxford, Chemistry Research Laboratory, Mansfield Road, Oxford, OX1 3TA, UK.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 218.29 kDa 
• Atom Count: 15,336 
• Modelled Residue Count: 1,807 
• Deposited Residue Count: 1,896 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
ALPHA, ALPHA-TREHALOSE-PHOSPHATE SYNTHASE [UDP-FORMING]	A, B, C, D	474	Escherichia coli K-12	Mutation(s): 0  EC: 2.4.1.15
UniProt
Find proteins for P31677 (Escherichia coli (strain K12)) Explore P31677  Go to UniProtKB:  P31677

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
VDO	I [auth A], M [auth B], O [auth C], Q [auth D]	[(1R,2R,3S,4S,5S)-2,3,4-TRIHYDROXY-5-{[(1S,4R,5S,6S)-4,5,6-TRIHYDROXY-3-(HYDROXYMETHYL)CYCLOHEX-2-EN-1-YL]AMINO}CYCLOHEXYL]METHYL DIHYDROGEN PHOSPHATE C14 H26 N O11 P ZKSTYMJGEHZSFH-MBABXGOBSA-N
UDP	H [auth A], L [auth B], N [auth C], P [auth D]	URIDINE-5'-DIPHOSPHATE C9 H14 N2 O12 P2 XCCTYIAWTASOJW-XVFCMESISA-N
EDO	E [auth A], F [auth A], G [auth A], J [auth B], K [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
VDO	PDBBind:  2WTX	Ki: 1.30e+6 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.235 
• R-Value Work: 0.195 
• R-Value Observed: 0.197 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 104.515	α = 90
b = 120.287	β = 90
c = 173.786	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-02-23 
Deposition Author(s): Errey, J.C., Lee, S.S., Gibson, R.P., Martinez-Fleites, C., Barry, C.S., Jung, P.M.J., OSullivan, A., Davis, B.G., Davies, G.J.

Revision History  

• Version 1.0: 2010-02-23
  Type: Initial release
  
• Version 1.1: 2011-05-08
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description