MolNFT v1 · #36462 · protein
Structure of the complex of a glucoamylase from saccharomycopsis fibuligera with acarbose
2F6D · Glucoamylase GLU1: “Structure of the complex of a glucoamylase from saccharomycopsis fibuligera with acarbose”. X-ray diffraction, 4 ligands (AC1, GLC, NA), 3 pockets (best druggability 0.71). MolNFT v1 #36462 on GenesisL1: 3D…
- PDB
- 2F6D
- Type
- protein
- Length
- 492 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucoamylase GLU1
- EC
- 3.2.1.3
- UniProt
- P08017
- Ligands
- AC1, GLC, NA, PO4
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 51% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucoamylase GLU1 (EC 3.2.1.3) | protein | 492 | 51% helix, 7% strand | P08017 |
Ligands and binding sites
- AC1 · 4,6-dideoxy-4-{[(1S,4R,5S,6S)-4,5,6-trihydroxy-3-(hydroxymethyl)cyclohex-2-en-1-yl]amino}-alpha-D-glucopyranose · ligand · 2 copies · chains A
- GLC · alpha-D-glucopyranose · sugar · 4 copies · chains A
- NA · Sodium ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 55 | 0.71 | 0.98 | 17 | empty |
| 2 | 119 | 0.55 | 0.83 | 24 | GLC, AC1 |
| 3 | 70 | 0.46 | 0.82 | 18 | empty |
Compared structures
- 2F6D · Structure of the complex of a glucoamylase from Saccharomycopsis fibuligera with acarbose · the same entry in another collection · chain A against A, TM-score 1.00
- P08017 · AlphaFold monomer V2.0 prediction for glucoamylase GLU1 (P08017) · 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 P08017
- Elsewhere: RCSB PDB 2F6D · PDBe 2F6D · UniProt P08017
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