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.

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

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

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

Bie, H.Y., Yin, J., He, X., Kermode, A.R., James, M.N.G.

To be published.

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

Find similar proteins by:

(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35475
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B	Go to GlyGen: P35475-1
Sequence Annotations Expand
Reference Sequence

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	Interactions Focus chain C Focus chain E Interactions & Density Focus chain C Focus chain E
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	Interactions Focus chain D Interactions & Density Focus chain D
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	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G83161QT GlyCosmos: G83161QT GlyGen: G83161QT

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain O [auth B] MOL2 format, chain G [auth A] MOL2 format, chain O [auth B] mmCIF format, chain G [auth A] mmCIF format, chain O [auth B]	G [auth A], O [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain G [auth A] Focus chain O [auth B] Interactions & Density Focus chain G [auth A] Focus chain O [auth B]
IDR Query on IDR Download Ideal Coordinates CCD File SDF format, chain L [auth A] SDF format, chain X [auth B] MOL2 format, chain L [auth A] MOL2 format, chain X [auth B] mmCIF format, chain L [auth A] mmCIF format, chain X [auth B]	L [auth A], X [auth B]	alpha-L-idopyranuronic acid C₆ H₁₀ O₇ AEMOLEFTQBMNLQ-VCSGLWQLSA-N		Interactions Focus chain L [auth A] Focus chain X [auth B] Interactions & Density Focus chain L [auth A] Focus chain X [auth B]
TLA Query on TLA Download Ideal Coordinates CCD File SDF format, chain K [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] MOL2 format, chain K [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] mmCIF format, chain K [auth A] mmCIF format, chain V [auth B] mmCIF format, chain W [auth B]	K [auth A], V [auth B], W [auth B]	L(+)-TARTARIC ACID C₄ H₆ O₆ FEWJPZIEWOKRBE-JCYAYHJZSA-N		Interactions Focus chain K [auth A] Focus chain V [auth B] Focus chain W [auth B] Interactions & Density Focus chain K [auth A] Focus chain V [auth B] Focus chain W [auth B]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain N [auth A] MOL2 format, chain N [auth A] mmCIF format, chain N [auth A]	N [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain N [auth A] Interactions & Density Focus chain N [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain R [auth B] SDF format, chain S [auth B] SDF format, chain T [auth B] SDF format, chain U [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] MOL2 format, chain T [auth B] MOL2 format, chain U [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B] mmCIF format, chain T [auth B] mmCIF format, chain U [auth B]	H [auth A] I [auth A] J [auth A] P [auth B] Q [auth B] 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		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain S [auth B] Focus chain T [auth B] Focus chain U [auth B]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain Y [auth B] MOL2 format, chain M [auth A] MOL2 format, chain Y [auth B] mmCIF format, chain M [auth A] mmCIF format, chain Y [auth B]	M [auth A], Y [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain M [auth A] Focus chain Y [auth B] Interactions & Density Focus chain M [auth A] Focus chain Y [auth B]

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

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2015-01-14

Deposition Author(s):

Revision History (Full details and data files)

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
Version 2.2: 2024-11-20
Changes: Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

4OBR

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

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

Entity ID: 1

UniProt & NIH Common Fund Data Resources

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Entity ID: 3

Glycosylation Resources

Entity ID: 4

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)