Research workbench
Crystal structure of the intramolecular trans-sialidase from ruminococcus gnavus in complex with oseltamivir carboxylate
Analyse Crystal structure of the intramolecular trans-sialidase from ruminococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X49
- Type
- protein
- Length
- 489 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anhydrosialidase
- UniProt
- V8BWT1
- Ligands
- ACE, G39, CA
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anhydrosialidase | protein | 489 | 4% helix, 44% strand | V8BWT1 |
Ligands and binding sites
- ACE · Acetyl group · ligand · 3 copies · chains A
- G39 · (3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy) cyclohex-1-ene-1-carboxylic acid · ligand · chains A
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 279 | 0.63 | 0.81 | 35 | empty |
| 2 | 227 | 0.60 | 0.80 | 30 | G39, GOL |
| 3 | 53 | 0.37 | 0.80 | 16 | GOL |
| 4 | 63 | 0.30 | 0.75 | 17 | empty |
| 5 | 77 | 0.30 | 0.72 | 18 | empty |
Compared structures
- 4X49 · Crystal structure of the intramolecular trans-sialidase from Ruminococcus gnavus in… · 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 V8BWT1
- Elsewhere: RCSB PDB 4X49 · PDBe 4X49 · UniProt V8BWT1
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