Research workbench
Crystal structure of the intramolecular trans-sialidase from ruminococcus gnavus in complex with 2,7-anhydro-NEU5AC
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
- 4X4A
- Type
- protein
- Length
- 485 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anhydrosialidase
- UniProt
- V8BWT1
- Ligands
- SKD, ACE, PO4
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anhydrosialidase | protein | 485 | 3% helix, 45% strand | V8BWT1 |
Ligands and binding sites
- SKD · 2-acetylamino-7-(1,2-dihydroxy-ethyl)-3-hydroxy-6,8-dioxa-bicyclo[3.2.1]octane-5-carboxylic acid · ligand · chains A
- ACE · Acetyl group · ligand · chains A
- PO4 · Phosphate ion · ion · chains A
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 264 | 0.61 | 0.80 | 38 | empty |
| 2 | 220 | 0.59 | 0.81 | 31 | SKD |
| 3 | 168 | 0.44 | 0.74 | 27 | empty |
Compared structures
- 4X4A · 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 4X4A · PDBe 4X4A · UniProt V8BWT1
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