2WNF

Crystal Structure of a Mammalian Sialyltransferase in complex with Gal-beta-1-3GalNAc-ortho-nitrophenol

• PDB DOI: https://doi.org/10.2210/pdb2WNF/pdb

• Classification: TRANSFERASE
• Organism(s): Sus scrofa
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-07-09 Released: 2009-10-13 
• Deposition Author(s): Rao, F.V., Rich, J.R., Raikic, B., Wakarchuk, W.W., Withers, S.G., Strynadka, N.C.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.195 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 

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: 35.27 kDa 
• Atom Count: 2,699 
• Modelled Residue Count: 272 
• Deposited Residue Count: 298 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
CMP-N-ACETYLNEURAMINATE-BETA-GALACTOSAMIDE-ALPHA-2,3-SIALYLTRANSFERASE	A	298	Sus scrofa	Mutation(s): 0  EC: 2.4.99.4
UniProt
Find proteins for Q02745 (Sus scrofa) Explore Q02745  Go to UniProtKB:  Q02745

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-galactopyranose-(1-3)-2-acetamido-2-deoxy-alpha-D-galactopyranose	B	2		N/A
Glycosylation Resources
GlyTouCan:  G00031MO GlyCosmos:  G00031MO GlyGen:  G00031MO

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CG3	C [auth A]	HYDROXY(2-HYDROXYPHENYL)OXOAMMONIUM C6 H6 N O3 CQQWRROYUSGJIU-UHFFFAOYSA-O

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
MSE	A	L-PEPTIDE LINKING	C5 H11 N O2 Se		MET

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900084	B	Thomsen-Friedenreich antigen	Oligosaccharide / Antigen

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.25 Å
• R-Value Free: 0.195 
• R-Value Work: 0.180 
• R-Value Observed: 0.181 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.987	α = 90
b = 78.347	β = 90
c = 99.191	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-10-13 
Deposition Author(s): Rao, F.V., Rich, J.R., Raikic, B., Wakarchuk, W.W., Withers, S.G., Strynadka, N.C.J.

Revision History  

• Version 1.0: 2009-10-13
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2011-11-16
  Changes: Database references, Other
• Version 1.3: 2015-05-20
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Other, Structure summary
• Version 2.1: 2023-12-13
  Changes: Data collection, Database references, Refinement description, Structure summary