1DOG
REFINED STRUCTURE FOR THE COMPLEX OF 1-DEOXYNOJIRIMYCIN WITH GLUCOAMYLASE FROM (ASPERGILLUS AWAMORI) VAR. X100 TO 2.4 ANGSTROMS RESOLUTION
- PDB DOI: https://doi.org/10.2210/pdb1DOG/pdb
- Classification: HYDROLASE
- Organism(s): Aspergillus awamori
- Mutation(s): No 
- Deposited: 1993-01-12 Released: 1994-01-31 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Observed: 0.119 
wwPDB Validation   3D Report Full Report
This is version 2.0 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 |
GLUCOAMYLASE-471 | 470 | Aspergillus awamori | Mutation(s): 0  EC: 3.2.1.3 | ||
UniProt | |||||
Find proteins for P69327 (Aspergillus awamori) Explore P69327  Go to UniProtKB:  P69327 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P69327 | ||||
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-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose | B | 5 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G42227JK GlyCosmos:  G42227JK GlyGen:  G42227JK |
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-(1-3)-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 | 8 | N-Glycosylation | ||
Glycosylation Resources | |||||
GlyTouCan:  G83582BK GlyCosmos:  G83582BK GlyGen:  G83582BK |
Small Molecules
Ligands 2 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
MAN Query on MAN | D [auth A] E [auth A] F [auth A] G [auth A] H [auth A] | alpha-D-mannopyranose C6 H12 O6 WQZGKKKJIJFFOK-PQMKYFCFSA-N | |||
NOJ Query on NOJ | N [auth A], O [auth A] | 1-DEOXYNOJIRIMYCIN C6 H13 N O4 LXBIFEVIBLOUGU-JGWLITMVSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Observed: 0.119 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 116.6 | α = 90 |
b = 103.6 | β = 90 |
c = 48.3 | γ = 90 |
Software Name | Purpose |
---|---|
PROLSQ | refinement |
Entry History 
Deposition Data
- Released Date: 1994-01-31  Deposition Author(s): Harris, E., Aleshin, A., Firsov, L., Honzatko, R.B.
Revision History (Full details and data files)
- Version 1.0: 1994-01-31
Type: Initial release - Version 1.1: 2008-03-24
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance - Version 1.3: 2017-11-29
Changes: Derived calculations, Other - Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary