3S5Y
Pharmacological Chaperoning in Human alpha-Galactosidase
- PDB DOI: https://doi.org/10.2210/pdb3S5Y/pdb
- Classification: HYDROLASE/HYDROLASE INHIBITOR
- 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: 2.10 Å
- R-Value Free: 0.230 
- R-Value Work: 0.194 
- R-Value Observed: 0.195 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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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 |
beta-D-xylopyranose-(1-2)-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 | D | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G06206UV GlyCosmos:  G06206UV GlyGen:  G06206UV |
Entity ID: 4 | |||||
---|---|---|---|---|---|
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 | E | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G11971MR GlyCosmos:  G11971MR GlyGen:  G11971MR |
Entity ID: 5 | |||||
---|---|---|---|---|---|
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 | F | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G71469XA GlyCosmos:  G71469XA GlyGen:  G71469XA |
Entity ID: 6 | |||||
---|---|---|---|---|---|
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 | G | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G18638YB GlyCosmos:  G18638YB GlyGen:  G18638YB |
Small Molecules
Ligands 5 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
2PE Query on 2PE | I [auth A], L [auth B], M [auth B], N [auth B], P [auth B] | NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N | |||
NAG Query on NAG | J [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
DGJ Query on DGJ | H [auth A], K [auth B] | (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol C6 H13 N O4 LXBIFEVIBLOUGU-DPYQTVNSSA-N | |||
EDO Query on EDO | O [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N | |||
ACY Query on ACY | Q [auth B], R [auth B] | ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.10 Å
- R-Value Free: 0.230 
- R-Value Work: 0.194 
- R-Value Observed: 0.195 
- Space Group: P 21 21 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 136.813 | α = 90 |
b = 182.635 | β = 90 |
c = 47.73 | γ = 90 |
Software Name | Purpose |
---|---|
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
HKL-2000 | data reduction |
AMoRE | phasing |
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: 2012-04-04
Changes: Structure summary - 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