MolNFT v1 · #54781 · protein
The aspergillus fumigatus sialidase is a kdnase: structural and mechanistic insights
2XZI · Extracellular SIALIDASE/NEURAMINIDASE, putative: “The aspergillus fumigatus sialidase is a kdnase: structural and mechanistic insights”. X-ray diffraction, 3 ligands (KDM, NA, NO2), 4 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 2XZI
- 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
- KDM, NA, NO2
- Pockets
- 4 · best druggability 0.79
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, 43% strand | Q4WQS0 |
Ligands and binding sites
- KDM · deamino-alpha-neuraminic acid · ligand · 4 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
- NO2 · Nitrite 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
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 703 | 0.79 | 0.83 | 70 | empty |
| 2 | 394 | 0.67 | 0.80 | 35 | empty |
| 3 | 255 | 0.57 | 0.78 | 45 | KDM, GOL |
| 4 | 246 | 0.56 | 0.78 | 39 | KDM |
Interfaces
1 interface between chains.
- A–B · 495 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2XZI · 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 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 Q4WQS0
- Elsewhere: RCSB PDB 2XZI · PDBe 2XZI · UniProt Q4WQS0
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.