3S5Z
Pharmacological Chaperoning in Human alpha-Galactosidase
- PDB DOI: https://doi.org/10.2210/pdb3S5Z/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Nicotiana benthamiana
- Mutation(s): No 
- Deposited: 2011-05-23 Released: 2012-01-04 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.234 
- R-Value Work: 0.210 
- R-Value Observed: 0.211 
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-galactosidase A | 398 | Homo sapiens | Mutation(s): 0  Gene Names: GLA EC: 3.2.1.22 | ||
UniProt & NIH Common Fund Data Resources | |||||
Find proteins for P06280 (Homo sapiens) Explore P06280  Go to UniProtKB:  P06280 | |||||
PHAROS:  P06280 GTEx:  ENSG00000102393  | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P06280 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-xylopyranose-(1-2)-[alpha-D-mannopyranose-(1-3)][alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | C | 7 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G26295XE GlyCosmos:  G26295XE GlyGen:  G26295XE |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose | D | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G11971MR GlyCosmos:  G11971MR GlyGen:  G11971MR |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-xylopyranose-(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 | E | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G71469XA GlyCosmos:  G71469XA GlyGen:  G71469XA |
Entity ID: 5 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-3)]2-acetamido-2-deoxy-beta-D-glucopyranose | F | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G18638YB GlyCosmos:  G18638YB GlyGen:  G18638YB |
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | I [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
GAL Query on GAL | H [auth A], K [auth B] | beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N | |||
GLA Query on GLA | G [auth A], J [auth B] | alpha-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-PHYPRBDBSA-N | |||
GOL Query on GOL | L [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.00 Å
- R-Value Free: 0.234 
- R-Value Work: 0.210 
- R-Value Observed: 0.211 
- Space Group: C 2 2 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 89.313 | α = 90 |
b = 140.606 | β = 90 |
c = 182.486 | γ = 90 |
Software Name | Purpose |
---|---|
SCALEPACK | data scaling |
AMoRE | phasing |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
DENZO | data reduction |
Entry History 
Deposition Data
- Released Date: 2012-01-04  Deposition Author(s): Guce, A.I., Clark, N.E., Garman, S.C.
Revision History (Full details and data files)
- Version 1.0: 2012-01-04
Type: Initial release - Version 1.1: 2017-11-08
Changes: Advisory, Refinement description - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary