3LRK

Structure of alfa-galactosidase (MEL1) from Saccharomyces cerevisiae

• PDB DOI: https://doi.org/10.2210/pdb3LRK/pdb

• Classification: HYDROLASE
• Organism(s): Saccharomyces cerevisiae
• Expression System: Saccharomyces cerevisiae
• Mutation(s): Yes 


• Deposited: 2010-02-11 Released: 2010-06-30 
• Deposition Author(s): Fernandez-Leiro, R., Pereira-Rodriguez, A., Cerdan, M.E., Becerra, M., Sanz-Aparicio, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.234 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 

Biological Assembly 1  

Global Symmetry: Cyclic - C4  (Explore in 3D)
Global Stoichiometry: Homo 4-mer - A4 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 55.37 kDa 
• Atom Count: 4,097 
• Modelled Residue Count: 452 
• Deposited Residue Count: 479 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Alpha-galactosidase 1	A	479	Saccharomyces cerevisiae	Mutation(s): 1  Gene Names: MEL1 EC: 3.2.1.22
UniProt
Find proteins for P04824 (Saccharomyces cerevisiae) Explore P04824  Go to UniProtKB:  P04824

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose	B	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G79924RM GlyCosmos:  G79924RM GlyGen:  G79924RM

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	C	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	D [auth A], E [auth A], F [auth A], G [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
BTB	L [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
GOL	H [auth A], I [auth A], J [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
NA	K [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.95 Å
• R-Value Free: 0.234 
• R-Value Work: 0.204 
• R-Value Observed: 0.205 
• Space Group: P 4 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.243	α = 90
b = 101.243	β = 90
c = 111.521	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-06-30 
Deposition Author(s): Fernandez-Leiro, R., Pereira-Rodriguez, A., Cerdan, M.E., Becerra, M., Sanz-Aparicio, J.

Revision History  

• Version 1.0: 2010-06-30
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2021-10-13
  Changes: Database references, Structure summary
• Version 2.2: 2023-09-06
  Changes: Data collection, Refinement description