6HZN

Crystal structure of human dermatan sulfate epimerase 1

• PDB DOI: https://doi.org/10.2210/pdb6HZN/pdb

• Classification: ISOMERASE
• Organism(s): Homo sapiens
• Expression System: Homo sapiens
• Mutation(s): No 


• Deposited: 2018-10-23 Released: 2020-01-22 
• Deposition Author(s): Hasan, M., Unge, J., Westergren-Thorsson, G., Ellervik, U., Mueller, U., Malmstrom, A., Tykesson, E.
• Funding Organization(s): Swedish Research Council

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.209 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 

Starting Model: other

Literature

The structure of human dermatan sulfate epimerase 1 emphasizes the importance of C5-epimerization of glucuronic acid in higher organisms

Hasan, M., Khakzad, H., Happonen, L., Sundin, A., Unge, J., Mueller, U., Malmstrom, J., Westergren-Thorsson, G., Malmstrom, L., Ellervik, U., Malmstrom, A., Tykesson, E.

(2020) Chem Sci 

• DOI: https://doi.org/10.1039/D0SC05971D

Biological Assembly 1  

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

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

Biological Assembly Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 89.48 kDa 
• Atom Count: 6,304 
• Modelled Residue Count: 743 
• Deposited Residue Count: 761 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Dermatan-sulfate epimerase	A	761	Homo sapiens	Mutation(s): 0  Gene Names: DSE, SART2 EC: 5.1.3.19
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UL01 (Homo sapiens) Explore Q9UL01  Go to UniProtKB:  Q9UL01
PHAROS:  Q9UL01 GTEx:  ENSG00000111817
Glycosylation
Glycosylation Sites: 4		Go to GlyGen: Q9UL01-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MES	G [auth A], H [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
MN	F [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.41 Å
• R-Value Free: 0.209 
• R-Value Work: 0.176 
• R-Value Observed: 0.177 
• Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 182.676	α = 90
b = 213.914	β = 90
c = 86.945	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
MxCuBE	data collection
XDS	data reduction
Aimless	data scaling
PHENIX	model building
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2020-01-22 
Deposition Author(s): Hasan, M., Unge, J., Westergren-Thorsson, G., Ellervik, U., Mueller, U., Malmstrom, A., Tykesson, E.

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Funding Organization	Location	Grant Number
Swedish Research Council	Sweden	2012-02631
Swedish Research Council	Sweden	--

Revision History  

• Version 1.0: 2020-01-22
  Type: Initial release
  
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2020-12-16
  Changes: Database references, Derived calculations, Structure summary
• Version 2.2: 2024-05-01
  Changes: Advisory, Data collection, Database references, Refinement description