4OBR

Crystal structure of human alpha-L-iduronidase complex with alpha-L-iduronic acid

• PDB DOI: https://doi.org/10.2210/pdb4OBR/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Arabidopsis thaliana
• Mutation(s): No 


• Deposited: 2014-01-07 Released: 2015-01-14 
• Deposition Author(s): Bie, H.Y., Yin, J., He, X., Kermode, A.R., James, M.N.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.239 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 

Biological Assembly 1  

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

Biological assembly 1 generated by PISA (software)

Biological Assembly 2  

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

Biological assembly 2 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 145.7 kDa 
• Atom Count: 10,073 
• Modelled Residue Count: 1,201 
• Deposited Residue Count: 1,254 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-L-iduronidase	A, B	627	Homo sapiens	Mutation(s): 0  Gene Names: IDUA EC: 3.2.1.76
UniProt & NIH Common Fund Data Resources
Find proteins for P35475 (Homo sapiens) Explore P35475  Go to UniProtKB:  P35475
PHAROS:  P35475 GTEx:  ENSG00000127415

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	C, E	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	D	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-3)]alpha-D-mannopyranose-(1-6)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	9		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G83161QT GlyCosmos:  G83161QT GlyGen:  G83161QT

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth A], O [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
IDR	L [auth A], X [auth B]	alpha-L-idopyranuronic acid C6 H10 O7 AEMOLEFTQBMNLQ-VCSGLWQLSA-N
TLA	K [auth A], V [auth B], W [auth B]	L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N
SO4	N [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	H [auth A], I [auth A], J [auth A], P [auth B], Q [auth B], R [auth B], S [auth B], T [auth B], U [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
CL	M [auth A], Y [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.46 Å
• R-Value Free: 0.239 
• R-Value Work: 0.202 
• R-Value Observed: 0.204 
• Space Group: H 3

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 258.94	α = 90
b = 258.94	β = 90
c = 71.53	γ = 120

Software Package:

Software Name	Purpose
MxDC	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-01-14 
Deposition Author(s): Bie, H.Y., Yin, J., He, X., Kermode, A.R., James, M.N.G.

Revision History  

• Version 1.0: 2015-01-14
  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: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary