3HG4
Human alpha-galactosidase catalytic mechanism 3. Covalent intermediate
- PDB DOI: https://doi.org/10.2210/pdb3HG4/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Homo sapiens
- Mutation(s): No 
- Deposited: 2009-05-13 Released: 2009-11-24 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.221 
- R-Value Work: 0.165 
- R-Value Observed: 0.166 
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 |
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose | C, F | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB |
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, G | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO |
Small Molecules
Ligands 5 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | L [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
7JZ Query on 7JZ | H [auth A], M [auth B] | 2-deoxy-2,2-difluoro-beta-D-lyxo-hexopyranose C6 H10 F2 O5 SHBCJQOMZTUYEL-MGCNEYSASA-N | |||
GAL Query on GAL | N [auth B] | beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N | |||
SO4 Query on SO4 | I [auth A], O [auth B], P [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L | |||
ACY Query on ACY | J [auth A], K [auth A], Q [auth B], R [auth B] | ACETIC ACID C2 H4 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.221 
- R-Value Work: 0.165 
- R-Value Observed: 0.166 
- Space Group: P 32 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 90.218 | α = 90 |
b = 90.218 | β = 90 |
c = 216.615 | γ = 120 |
Software Name | Purpose |
---|---|
DENZO | data reduction |
SCALEPACK | data scaling |
REFMAC | refinement |
PDB_EXTRACT | data extraction |
HKL-2000 | data collection |
HKL-2000 | data reduction |
HKL-2000 | data scaling |
Entry History 
Deposition Data
- Released Date: 2009-11-24  Deposition Author(s): Guce, A.I., Clark, N.E., Garman, S.C.
Revision History (Full details and data files)
- Version 1.0: 2009-11-24
Type: Initial release - Version 1.1: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.2: 2017-11-01
Changes: 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: 2024-04-03
Changes: Data collection, Database references, Refinement description, Structure summary