Research workbench
Structural evaluation R171L mutant of the aspergillus fumigatus kdnase (sialidase)
Analyse Structural evaluation R171L mutant of the aspergillus fumigatus kdnase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M4V
- 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
- DAN, NA, NO3
- Pockets
- 5 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Extracellular SIALIDASE/NEURAMINIDASE, putative (EC 3.2.1.18) | protein | 385 | 5% helix, 44% strand | Q4WQS0 |
| B | Extracellular SIALIDASE/NEURAMINIDASE, putative (EC 3.2.1.18) | protein | 384 | 4% helix, 44% strand | Q4WQS0 |
Ligands and binding sites
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · chains A
- NA · Sodium ion · metal · chains A
- NO3 · Nitrate ion · ion · 4 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 730 | 0.79 | 0.83 | 65 | GOL |
| 2 | 429 | 0.68 | 0.80 | 33 | empty |
| 3 | 298 | 0.63 | 0.80 | 50 | NO3 |
| 4 | 326 | 0.62 | 0.79 | 50 | DAN |
| 5 | 51 | 0.32 | 0.78 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 456 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 4M4V · Structural evaluation R171L mutant of the aspergillus fumigatus kdnase (sialidase) · 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 4M4V · PDBe 4M4V · UniProt Q4WQS0
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