MolNFT v1 · #111614 · protein
Crystal structure of streptococcus pneumoniae nanc, complex with NEU5AC and NEU5AC2EN following soaking with 3'SL
4YW1 · Neuraminidase C: “Crystal structure of streptococcus pneumoniae nanc, complex with NEU5AC and NEU5AC2EN following soaking with…”. X-ray diffraction, 3 ligands (DAN, SIA, PO4), 17 pockets (best druggability 0.67). MolNFT v1 #111614…
- PDB
- 4YW1
- 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
- DAN, SIA, PO4
- Pockets
- 17 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 4% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Neuraminidase C (EC 3.2.1.18) | protein | 659 | 4% helix, 45% strand | A0A0H2UQE4 |
Ligands and binding sites
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic acid · ligand · chains B
- SIA · N-acetyl-alpha-neuraminic acid · sugar · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.67 | 0.97 | 18 | empty |
| 2 | 446 | 0.65 | 0.78 | 31 | empty |
| 3 | 220 | 0.64 | 0.83 | 33 | DAN |
| 4 | 233 | 0.54 | 0.77 | 28 | PO4 |
| 5 | 226 | 0.54 | 0.78 | 31 | empty |
Interfaces
1 interface between chains.
- A–B · 274 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4YW1 · Crystal Structure of Streptococcus pneumoniae NanC, complex with Neu5Ac and Neu5Ac2en… · 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 4YW1 · PDBe 4YW1 · UniProt A0A0H2UQE4
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