4PXQ

Crystal structure of D-glucuronyl C5-epimerase in complex with heparin hexasaccharide

• PDB DOI: https://doi.org/10.2210/pdb4PXQ/pdb

• Classification: ISOMERASE
• Organism(s): Danio rerio
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-03-24 Released: 2015-01-14 
• Deposition Author(s): Ke, J., Qin, Y., Gu, X., Tan, J., Brunzelle, J.S., Xu, H.E., Ding, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.222 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

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)

Macromolecule Content

• Total Structure Weight: 135.74 kDa 
• Atom Count: 9,275 
• Modelled Residue Count: 1,031 
• Deposited Residue Count: 1,170 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
D-glucuronyl C5 epimerase B	A, B	585	Danio rerio	Mutation(s): 0  Gene Names: glce, glceb, Hsepi EC: 5.1.3.17
UniProt
Find proteins for F1QR43 (Danio rerio) Explore F1QR43  Go to UniProtKB:  F1QR43

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
4-deoxy-2-O-sulfo-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose	C, D	6		N/A
Glycosylation Resources
GlyTouCan:  G26920WX GlyCosmos:  G26920WX

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.222 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.606	α = 90
b = 200.982	β = 90
c = 46.561	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELXS	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-14 
Deposition Author(s): Ke, J., Qin, Y., Gu, X., Tan, J., Brunzelle, J.S., Xu, H.E., Ding, K.

Revision History  

• Version 1.0: 2015-01-14
  Type: Initial release
  
• Version 1.1: 2015-02-25
  Changes: Database references
• Version 1.2: 2015-03-18
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2024-02-28
  Changes: Data collection, Database references, Structure summary