4KGL
Crystal structure of human alpha-L-iduronidase complex with [2R,3R,4R,5S]-2-carboxy-3,4,5-trihydroxy-piperidine
- PDB DOI: https://doi.org/10.2210/pdb4KGL/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- Organism(s): Homo sapiens
- Expression System: Arabidopsis thaliana
- Mutation(s): No 
- Deposited: 2013-04-29 Released: 2013-09-18 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.70 Å
- R-Value Free: 0.254 
- R-Value Work: 0.204 
- R-Value Observed: 0.206 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Alpha-L-iduronidase | 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 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
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 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | G [auth A], J [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
IDJ Query on IDJ | I [auth A], P [auth B] | (2R,3R,4R,5S)-3,4,5-trihydroxypiperidine-2-carboxylic acid C6 H11 N O5 ZHFMVVUVCALAMY-NRXMZTRTSA-N | |||
TLA Query on TLA | O [auth B] | L(+)-TARTARIC ACID C4 H6 O6 FEWJPZIEWOKRBE-JCYAYHJZSA-N | |||
GOL Query on GOL | H [auth A], K [auth B], L [auth B], M [auth B], N [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.70 Å
- R-Value Free: 0.254 
- R-Value Work: 0.204 
- R-Value Observed: 0.206 
- Space Group: H 3
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 259.359 | α = 90 |
b = 259.359 | β = 90 |
c = 71.568 | γ = 120 |
Software Name | Purpose |
---|---|
HKL-2000 | data collection |
PHASER | phasing |
REFMAC | refinement |
HKL-2000 | data reduction |
SCALEPACK | data scaling |
Entry History 
Deposition Data
- Released Date: 2013-09-18  Deposition Author(s): Bie, H., Yin, J., He, X., Kermode, A.R., Goddard-Borger, E.D., Withers, S.G., James, M.N.G.
Revision History (Full details and data files)
- Version 1.0: 2013-09-18
Type: Initial release - Version 1.1: 2013-09-25
Changes: Database references - Version 1.2: 2013-11-06
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: 2023-09-20
Changes: Data collection, Database references, Refinement description, Structure summary