4E5Y | pdb_00004e5y

Structure of human FX protein, the key enzyme in the biosynthesis of GDP-L-fucose

• PDB DOI: https://doi.org/10.2210/pdb4E5Y/pdb

• Classification: OXIDOREDUCTASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-15 Released: 2013-04-17 
• Deposition Author(s): Zhou, H., He, J.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free: 
  0.291 (Depositor), 0.290 (DCC) 
• R-Value Work: 
  0.232 (Depositor), 0.240 (DCC) 
• R-Value Observed: 
  0.234 (Depositor) 

Literature

Structure of human FX protein, the key enzyme in the biosynthesis of GDP-L-fucose

Zhou, H., He, J.H.

To be published.

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: 146.72 kDa 
• Atom Count: 9,903 
• Modeled Residue Count: 1,224 
• Deposited Residue Count: 1,284 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
GDP-L-fucose synthase	A, B, C, D	321	Homo sapiens	Mutation(s): 0  Gene Names: TSTA3, SDR4E1 EC: 1.1.1.271
UniProt & NIH Common Fund Data Resources
Find proteins for Q13630 (Homo sapiens) Explore Q13630  Go to UniProtKB:  Q13630
PHAROS:  Q13630 GTEx:  ENSG00000104522

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NDP	E [auth A], F [auth B], G [auth C], H [auth D]	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE C21 H30 N7 O17 P3 ACFIXJIJDZMPPO-NNYOXOHSSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.37 Å
• R-Value Free:  0.291 (Depositor), 0.290 (DCC) 
• R-Value Work:  0.232 (Depositor), 0.240 (DCC) 
• R-Value Observed: 0.234 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 85.772	α = 90
b = 136.44	β = 90
c = 139.849	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHENIX	model building
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-17 
Deposition Author(s): Zhou, H., He, J.H.

Revision History  

• Version 1.0: 2013-04-17
  Type: Initial release
  
• Version 1.1: 2024-03-20
  Changes: Data collection, Database references, Derived calculations