6HZN | pdb_00006hzn

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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free:
0.209 (Depositor), 0.214 (DCC)
R-Value Work:
0.176 (Depositor), 0.181 (DCC)
R-Value Observed:
0.177 (Depositor)

Starting Model: other
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.3 of the entry. See complete history.

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

Macromolecule Content

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

Macromolecules

Find similar proteins by:

| 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9UL01
Glycosylation
Glycosylation Sites: 4	Glycosylation Focus chain A	Go to GlyGen: Q9UL01-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

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

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	D 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	Interactions Focus chain C Interactions & Density Focus chain C
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain E [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A]	D [auth A], E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain D [auth A] Focus chain E [auth A] Interactions & Density Focus chain D [auth A] Focus chain E [auth A]
MES Query on MES Download:Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A]	G [auth A], H [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C₆ H₁₃ N O₄ S SXGZJKUKBWWHRA-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Interactions & Density Focus chain G [auth A] Focus chain H [auth A]
MN Query on MN Download:Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.41 Å
R-Value Free: 0.209 (Depositor), 0.214 (DCC)
R-Value Work: 0.176 (Depositor), 0.181 (DCC)
R-Value Observed: 0.177 (Depositor)

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

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2020-01-22

Deposition Author(s):

Hasan, M.

Unge, J.

Westergren-Thorsson, G.

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

Revision History (Full details and data files)

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
Version 2.3: 2024-11-13
Changes: Structure summary