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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
- 5FQF
- Type
- protein
- Length
- 1,163 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-N-acetylgalactosaminidase
- UniProt
- A0A0H2YNR7
- Ligands
- NGA
- Pockets
- 16 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-N-acetylgalactosaminidase | protein | 583 | 32% helix, 28% strand | A0A0H2YNR7 |
| B | Beta-N-acetylgalactosaminidase | protein | 580 | 31% helix, 28% strand | A0A0H2YNR7 |
Ligands and binding sites
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 4 copies · chains A, B
- FMT · Formic acid · additive · 15 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 271 | 0.74 | 0.87 | 40 | NGA |
| 2 | 257 | 0.73 | 0.87 | 40 | NGA |
| 3 | 263 | 0.71 | 0.86 | 47 | FMT |
| 4 | 341 | 0.65 | 0.80 | 42 | FMT |
| 5 | 293 | 0.62 | 0.80 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 715 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5FQF · 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 5FQF · PDBe 5FQF · UniProt A0A0H2YNR7
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