Research workbench
Crystal structure of streptococcus pneumoniae nanc, in complex with oseltamivir.
Analyse Crystal structure of streptococcus pneumoniae nanc, in 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
- 4YZ3
- Type
- protein
- Length
- 1,310 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Neuraminidase
- EC
- 3.2.1.18
- UniProt
- Q97Q99
- Ligands
- G39, SO4
- Pockets
- 14 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Neuraminidase (EC 3.2.1.18) | protein | 654 | 3% helix, 45% strand | Q97Q99 |
| B | Neuraminidase (EC 3.2.1.18) | protein | 656 | 3% helix, 45% strand | Q97Q99 |
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
- SO4 · Sulfate ion · ion · 10 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.69 | 0.97 | 19 | empty |
| 2 | 65 | 0.69 | 0.96 | 23 | empty |
| 3 | 330 | 0.65 | 0.80 | 45 | G39 |
| 4 | 331 | 0.64 | 0.80 | 45 | G39 |
| 5 | 357 | 0.57 | 0.76 | 37 | empty |
Interfaces
1 interface between chains.
- A–B · 154 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4YZ3 · Crystal Structure of Streptococcus pneumoniae NanC, in complex with Oseltamivir. · 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 Q97Q99
- Elsewhere: RCSB PDB 4YZ3 · PDBe 4YZ3 · UniProt Q97Q99
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