MolNFT v1 · #111615 · protein
Crystal structure of streptococcus pneumoniae nanc, complex 6'SL
4YW2 · Neuraminidase C: “Crystal structure of streptococcus pneumoniae nanc, complex 6'SL”. X-ray diffraction, 3 ligands (GAL, SIA, PO4), 14 pockets (best druggability 0.65). MolNFT v1 #111615 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4YW2
- 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
- GAL, SIA, PO4
- Pockets
- 14 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neuraminidase C (EC 3.2.1.18) | protein | 659 | 4% helix, 46% strand | A0A0H2UQE4 |
Ligands and binding sites
- GAL · beta-D-galactopyranose · sugar · 2 copies
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 430 | 0.65 | 0.78 | 33 | empty |
| 2 | 282 | 0.56 | 0.77 | 35 | PO4 |
| 3 | 314 | 0.55 | 0.75 | 30 | empty |
| 4 | 231 | 0.54 | 0.77 | 32 | PO4 |
| 5 | 276 | 0.54 | 0.76 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 277 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 4YW2 · Crystal Structure of Streptococcus pneumoniae NanC, complex 6'SL · 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 4YW2 · PDBe 4YW2 · UniProt A0A0H2UQE4
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