Research workbench
Refined structure for the complex of 1-deoxynojirimycin with glucoamylase from (aspergillus awamori) var. X100 to 2.4 ångströms resolution
Analyse Refined structure for the complex of 1-deoxynojirimycin with glucoamylase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DOG
- Type
- protein
- Length
- 470 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucoamylase-471
- EC
- 3.2.1.3
- UniProt
- P23176
- Ligands
- NOJ, MAN, NAG, BMA
- Pockets
- 1 · best druggability 0.58
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucoamylase-471 (EC 3.2.1.3) | protein | 470 | 48% helix, 7% strand | P23176 |
Ligands and binding sites
- NOJ · 1-deoxynojirimycin · ligand · 2 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 17 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 116 | 0.58 | 0.84 | 21 | NOJ |
Modifications
Observed in the structure: 12 glycan, 3 disulfide (O-glycosylation, disulfide, N-glycosylation).
Compared structures
- 1DOG · Refined structure for the complex of 1-deoxynojirimycin with glucoamylase from… · the same entry in another collection · chain A against A, TM-score 1.00
- P23176 · AlphaFold monomer V2.0 prediction for glucoamylase I (P23176) · a predicted model of the same protein · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P23176
- Elsewhere: RCSB PDB 1DOG · PDBe 1DOG · UniProt P23176
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