5MGC
STRUCTURE OF E298Q-BETA-GALACTOSIDASE FROM ASPERGILLUS NIGER IN COMPLEX WITH 4-Galactosyl-lactose
- PDB DOI: https://doi.org/10.2210/pdb5MGC/pdb
- Classification: HYDROLASE
- Organism(s): Aspergillus niger CBS 513.88
- Expression System: Saccharomyces cerevisiae
- Mutation(s): Yes 
- Deposited: 2016-11-21 Released: 2017-04-19 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.204 
- R-Value Work: 0.169 
- R-Value Observed: 0.171 
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 |
Probable beta-galactosidase A | 1,013 | Aspergillus niger CBS 513.88 | Mutation(s): 1  Gene Names: lacA, An01g12150 EC: 3.2.1.23 | ||
UniProt | |||||
Find proteins for A2QAN3 (Aspergillus niger (strain ATCC MYA-4892 / CBS 513.88 / FGSC A1513)) Explore A2QAN3  Go to UniProtKB:  A2QAN3 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | A2QAN3 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[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 | B | 8 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G83582BK GlyCosmos:  G83582BK GlyGen:  G83582BK |
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-6)-[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 | C | 10 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G40702WU GlyCosmos:  G40702WU GlyGen:  G40702WU |
Entity ID: 4 | |||||
---|---|---|---|---|---|
Molecule | Chains | Length | 2D Diagram | Glycosylation | 3D Interactions |
alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(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 | D | 6 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G01760ZU GlyCosmos:  G01760ZU GlyGen:  G01760ZU |
Small Molecules
Ligands 1 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
NAG Query on NAG | F [auth A] G [auth A] H [auth A] I [auth A] J [auth A] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.204 
- R-Value Work: 0.169 
- R-Value Observed: 0.171 
- Space Group: P 1 21 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 59.627 | α = 90 |
b = 106.659 | β = 96.13 |
c = 84.425 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
XDS | data reduction |
Aimless | data scaling |
MOLREP | phasing |
Entry History 
Deposition Data
- Released Date: 2017-04-19  Deposition Author(s): Rico-Diaz, A., Ramirez-Escudero, M., Vizoso Vazquez, A., Cerdan, M.E., Becerra, M., Sanz-Aparicio, J.
Revision History (Full details and data files)
- Version 1.0: 2017-04-19
Type: Initial release - Version 1.1: 2017-06-28
Changes: Database references - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary - Version 2.1: 2024-01-17
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary