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The details of glycolipid glycan hydrolysis by the structural analysis of a family 123 glycoside hydrolase from clostridium perfringens
Analyse The details of glycolipid glycan hydrolysis by the structural analysis of a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FQG
- Type
- protein
- Length
- 583 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-N-acetylgalactosaminidase
- UniProt
- A0A0H2YNR7
- Ligands
- GAL, NGA
- Pockets
- 10 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-N-acetylgalactosaminidase | protein | 583 | 32% helix, 28% strand | A0A0H2YNR7 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · chains A
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · chains A
- FMT · Formic acid · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.61 | 0.80 | 39 | GAL, NGA |
| 2 | 308 | 0.61 | 0.79 | 33 | FMT |
| 3 | 213 | 0.55 | 0.78 | 25 | empty |
| 4 | 103 | 0.50 | 0.82 | 25 | empty |
| 5 | 91 | 0.40 | 0.78 | 20 | empty |
Compared structures
- 5FQG · The details of glycolipid glycan hydrolysis by the structural analysis of a family 123… · 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 A0A0H2YNR7
- Elsewhere: RCSB PDB 5FQG · PDBe 5FQG · UniProt A0A0H2YNR7
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