Research workbench
Crystal structure of streptococcus pneumoniae nanc, complex with oseltamivir carboxylate
Analyse Crystal structure of streptococcus pneumoniae nanc, complex with oseltamivir… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YW5
- Type
- protein
- Length
- 1,318 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase C
- EC
- 3.2.1.18
- UniProt
- A0A0H2UQE4
- Ligands
- G39
- Pockets
- 15 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neuraminidase C (EC 3.2.1.18) | protein | 659 | 5% helix, 44% strand | A0A0H2UQE4 |
Ligands and binding sites
- G39 · (3R,4R,5S)-4-(acetylamino)-5-amino-3-(pentan-3-yloxy) cyclohex-1-ene-1-carboxylic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 9 copies · chains A, B
- EDO · 1,2-ethanediol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.67 | 0.81 | 47 | G39, GOL |
| 2 | 295 | 0.67 | 0.82 | 40 | G39, GOL |
| 3 | 413 | 0.63 | 0.77 | 28 | empty |
| 4 | 280 | 0.53 | 0.75 | 32 | empty |
| 5 | 277 | 0.52 | 0.75 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 258 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4YW5 · Crystal Structure of Streptococcus pneumoniae NanC, complex with oseltamivir carboxylate · the same entry in another collection · 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 A0A0H2UQE4
- Elsewhere: RCSB PDB 4YW5 · PDBe 4YW5 · UniProt A0A0H2UQE4
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