MolNFT v1 · #148817 · protein
Crystal structure of penicillium oxalicum glucoamylase
6FHV: “Crystal structure of penicillium oxalicum glucoamylase”. X-ray diffraction, 2 ligands (NAG, BMA), 6 pockets (best druggability 0.77). MolNFT v1 #148817 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6FHV
- Type
- protein
- Length
- 585 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucoamylase
- EC
- 3.2.1.3
- UniProt
- S7ZIW0
- Ligands
- NAG, BMA
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucoamylase (EC 3.2.1.3) | protein | 585 | 40% helix, 13% strand | S7ZIW0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- B3P · 2-[3-(2-hydroxy-1,1-dihydroxymethyl-ethylamino)-propylamino]-2-hydroxymethyl-propane-1,3-diol · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 100 | 0.77 | 0.97 | 27 | empty |
| 2 | 91 | 0.59 | 0.87 | 19 | B3P |
| 3 | 88 | 0.44 | 0.79 | 15 | empty |
| 4 | 128 | 0.42 | 0.75 | 20 | empty |
| 5 | 117 | 0.39 | 0.75 | 22 | empty |
Modifications
Observed in the structure: 4 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6FHV · Crystal structure of Penicillium oxalicum Glucoamylase · the same entry in another collection · 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 S7ZIW0
- Elsewhere: RCSB PDB 6FHV · PDBe 6FHV · UniProt S7ZIW0
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