2YFO
GALACTOSIDASE DOMAIN OF ALPHA-GALACTOSIDASE-SUCROSE KINASE, AGASK, in complex with galactose
- PDB DOI: https://doi.org/10.2210/pdb2YFO/pdb
- Classification: HYDROLASE
- Organism(s): Mediterraneibacter gnavus E1
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No 
- Deposited: 2011-04-07 Released: 2011-09-28 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.35 Å
- R-Value Free: 0.142 
- R-Value Work: 0.124 
- R-Value Observed: 0.125 
This is version 1.3 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-SUCROSE KINASE AGASK | 720 | Mediterraneibacter gnavus E1 | Mutation(s): 0  EC: 3.2.1.22 | ||
UniProt | |||||
Find proteins for G4T4R7 (Ruminococcus gnavus) Explore G4T4R7  Go to UniProtKB:  G4T4R7 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | G4T4R7 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 6 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
GAL Query on GAL | JA [auth A] | beta-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-FPRJBGLDSA-N | |||
GLA Query on GLA | IA [auth A] | alpha-D-galactopyranose C6 H12 O6 WQZGKKKJIJFFOK-PHYPRBDBSA-N | |||
PGE Query on PGE | C [auth A], D [auth A], E [auth A], F [auth A] | TRIETHYLENE GLYCOL C6 H14 O4 ZIBGPFATKBEMQZ-UHFFFAOYSA-N | |||
PO4 Query on PO4 | G [auth A] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K | |||
GOL Query on GOL | B [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N | |||
NA Query on NA | AA [auth A] BA [auth A] CA [auth A] DA [auth A] EA [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.35 Å
- R-Value Free: 0.142 
- R-Value Work: 0.124 
- R-Value Observed: 0.125 
- Space Group: I 2 2 2
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 105.016 | α = 90 |
b = 111.603 | β = 90 |
c = 155.29 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
XDS | data reduction |
SCALA | data scaling |
REFMAC | phasing |
Entry History 
Deposition Data
- Released Date: 2011-09-28  Deposition Author(s): Sulzenbacher, G., Bruel, L., Tison-Cervera, M., Pujol, A., Nicoletti, C., Perrier, J., Galinier, A., Ropartz, D., Fons, M., Pompeo, F., Giardina, T.
Revision History (Full details and data files)
- Version 1.0: 2011-09-28
Type: Initial release - Version 1.1: 2011-11-23
Changes: Database references, Derived calculations, Other - Version 1.2: 2011-12-07
Changes: Database references - Version 1.3: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Other, Structure summary