Research workbench
Mutagenesis of the nucleophilic tyrosine in a bacterial sialidase to phenylalanine.
Analyse Mutagenesis of the nucleophilic tyrosine in a bacterial sialidase to… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1WCQ
- Type
- protein
- Length
- 1,801 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sialidase
- EC
- 3.2.1.18
- UniProt
- Q02834
- Ligands
- DAN, NA
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Sialidase (EC 3.2.1.18) | protein | 601 | 2% helix, 48% strand | Q02834 |
| C | Sialidase (EC 3.2.1.18) | protein | 599 | 4% helix, 48% strand | Q02834 |
Ligands and binding sites
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · 3 copies · chains A, B, C
- NA · Sodium ion · metal · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 7 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 213 | 0.71 | 0.88 | 35 | empty |
| 2 | 207 | 0.71 | 0.88 | 36 | empty |
| 3 | 201 | 0.69 | 0.87 | 32 | empty |
| 4 | 708 | 0.67 | 0.75 | 73 | empty |
| 5 | 506 | 0.65 | 0.77 | 58 | empty |
Interfaces
2 interfaces between chains.
- B–C · 427 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 375 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 1WCQ · Mutagenesis of the Nucleophilic Tyrosine in a Bacterial Sialidase to Phenylalanine. · the same entry in another collection · chain A against A, TM-score 1.00
- Q02834 · AlphaFold monomer V2.0 prediction for sialidase (Q02834) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q02834
- Elsewhere: RCSB PDB 1WCQ · PDBe 1WCQ · UniProt Q02834
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