Research workbench
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
- 5FQE
- Type
- protein
- Length
- 1,159 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Beta-N-acetylgalactosaminidase
- UniProt
- A0A0H2YNR7
- Ligands
- BR
- Pockets
- 14 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Beta-N-acetylgalactosaminidase | protein | 580 | 31% helix, 29% strand | A0A0H2YNR7 |
| B | Beta-N-acetylgalactosaminidase | protein | 579 | 31% helix, 28% strand | A0A0H2YNR7 |
Ligands and binding sites
- BR · Bromide ion · ion · 133 copies · chains A, B
- FMT · Formic acid · additive · 4 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1002 | 0.83 | 0.84 | 115 | BR, MPD |
| 2 | 478 | 0.76 | 0.85 | 51 | FMT, BR |
| 3 | 357 | 0.65 | 0.80 | 36 | BR |
| 4 | 315 | 0.63 | 0.79 | 36 | BR |
| 5 | 146 | 0.58 | 0.83 | 20 | BR |
Interfaces
1 interface between chains.
- A–B · 631 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 5FQE · 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 5FQE · PDBe 5FQE · UniProt A0A0H2YNR7
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.