Research workbench
The aspergillus fumigatus sialidase is a kdnase: structural and mechanistic insights
Analyse The aspergillus fumigatus sialidase is a kdnase: structural and mechanistic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XZK
- Type
- protein
- Length
- 769 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Extracellular SIALIDASE/NEURAMINIDASE, putative
- EC
- 3.2.1.18
- UniProt
- Q4WQS0
- Ligands
- K99, FKD, NA, CL, NO3
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Extracellular SIALIDASE/NEURAMINIDASE, putative (EC 3.2.1.18) | protein | 385 | 5% helix, 43% strand | Q4WQS0 |
| B | Extracellular SIALIDASE/NEURAMINIDASE, putative (EC 3.2.1.18) | protein | 384 | 5% helix, 44% strand | Q4WQS0 |
Ligands and binding sites
- K99 · (2R,3R,4R,5R,6S)-2,3-bis(fluoranyl)-4,5-bis(oxidanyl)-6-[(1R,2R)-1,2,3-tris(oxidanyl)propyl]oxane-2-carboxylic acid · ligand · 5 copies · chains A, B
- FKD · 3-deoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · chains A
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.77 | 0.88 | 40 | K99 |
| 2 | 411 | 0.68 | 0.81 | 34 | empty |
| 3 | 391 | 0.65 | 0.79 | 31 | empty |
| 4 | 277 | 0.57 | 0.77 | 42 | FKD, K99, CL |
| 5 | 245 | 0.56 | 0.78 | 41 | FKD, K99, CL |
Interfaces
1 interface between chains.
- A–B · 408 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2XZK · The aspergillus fumigatus sialidase is a kdnase: structural and mechanistic insights · the same entry in another collection · chain A against A, TM-score 1.00
- Q4WQS0 · AlphaFold monomer V2.0 prediction for exo-alpha-sialidase (Q4WQS0) · a predicted model of the same protein · chain B 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 Q4WQS0
- Elsewhere: RCSB PDB 2XZK · PDBe 2XZK · UniProt Q4WQS0
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