3TV8
Pharmacological Chaperoning in Human alpha-Galactosidase
- PDB DOI: https://doi.org/10.2210/pdb3TV8/pdb
- Classification: HYDROLASE
- Organism(s): Homo sapiens
- Expression System: Trichoplusia ni
- Mutation(s): Yes 
- Deposited: 2011-09-19 Released: 2012-01-04 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.64 Å
- R-Value Free: 0.239 
- R-Value Work: 0.201 
- R-Value Observed: 0.203 
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 | 404 | Homo sapiens | Mutation(s): 1  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-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | C | 3 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G15407YE GlyCosmos:  G15407YE GlyGen:  G15407YE |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
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 | D | 4 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G81315DD GlyCosmos:  G81315DD GlyGen:  G81315DD |
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
2PE Query on 2PE | H [auth A], I [auth A], O [auth B] | NONAETHYLENE GLYCOL C18 H38 O10 YZUUTMGDONTGTN-UHFFFAOYSA-N | |||
NAG Query on NAG | E [auth A], F [auth A], K [auth B], L [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
DGJ Query on DGJ | J [auth A], P [auth B] | (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol C6 H13 N O4 LXBIFEVIBLOUGU-DPYQTVNSSA-N | |||
SO4 Query on SO4 | G [auth A], M [auth B], N [auth B] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.64 Å
- R-Value Free: 0.239 
- R-Value Work: 0.201 
- R-Value Observed: 0.203 
- Space Group: P 32 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 90.465 | α = 90 |
b = 90.465 | β = 90 |
c = 216.544 | γ = 120 |
Software Name | Purpose |
---|---|
SCALEPACK | data scaling |
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): Rogich, J.J., 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 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Refinement description, Structure summary - Version 2.1: 2023-09-13
Changes: Data collection, Database references, Refinement description, Structure summary