Research workbench
Enhancing the receptor affinity of the sialic acid-binding domain of vibrio cholerae sialidase through multivalency
Analyse Enhancing the receptor affinity of the sialic acid-binding domain of vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2W68
- Type
- protein
- Length
- 582 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sialidase
- EC
- 3.2.1.18
- UniProt
- P0C6E9
- Ligands
- BGC, GAL, SIA, CA
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 11% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sialidase (EC 3.2.1.18) | protein | 195 | 11% helix, 51% strand | P0C6E9 |
| B | Sialidase (EC 3.2.1.18) | protein | 193 | 11% helix, 54% strand | P0C6E9 |
| C | Sialidase (EC 3.2.1.18) | protein | 194 | 11% helix, 52% strand | P0C6E9 |
Ligands and binding sites
- BGC · beta-D-glucopyranose · sugar · 3 copies · chains A
- GAL · beta-D-galactopyranose · sugar · 3 copies · chains A, B, C
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 3 copies · chains A, C, B
- CA · Calcium ion · metal · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 62 | 0.72 | 0.98 | 33 | empty |
| 2 | 485 | 0.63 | 0.76 | 71 | SIA |
| 3 | 293 | 0.56 | 0.77 | 30 | empty |
| 4 | 75 | 0.32 | 0.75 | 17 | SIA |
| 5 | 61 | 0.27 | 0.73 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–B · 791 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 343 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 159 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 2W68 · Enhancing the receptor affinity of the sialic acid-binding domain of vibrio cholerae… · the same entry in another collection · chain A against A, TM-score 1.00
- P0C6E9 · AlphaFold monomer V2.0 prediction for sialidase (P0C6E9) · a predicted model of the same protein · chain B against A, TM-score 0.98
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 P0C6E9
- Elsewhere: RCSB PDB 2W68 · PDBe 2W68 · UniProt P0C6E9
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