MolNFT v1 · #111716 · protein
Crystal structure of streptococcus pneumoniae nanc, in complex with 2- deoxy-2,3-didehydro-N-acetylneuraminic acid.
4YZ2 · Sialidase nanc: “Crystal structure of streptococcus pneumoniae nanc, in complex with 2- deoxy-2,3-didehydro-N-acetylneuraminic…”. X-ray diffraction, 2 ligands (DAN, SO4), 12 pockets (best druggability 0.68). MolNFT v1 #111716 on…
- PDB
- 4YZ2
- Type
- protein
- Length
- 1,311 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sialidase nanc
- EC
- 3.2.1.18
- UniProt
- Q97Q99
- Ligands
- DAN, SO4
- Pockets
- 12 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sialidase nanc (EC 3.2.1.18) | protein | 655 | 4% helix, 46% strand | Q97Q99 |
| B | Sialidase nanc (EC 3.2.1.18) | protein | 656 | 4% helix, 46% strand | Q97Q99 |
Ligands and binding sites
- DAN · 2-deoxy-2,3-dehydro-N-acetyl-neuraminic 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
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 72 | 0.68 | 0.94 | 25 | empty |
| 2 | 260 | 0.66 | 0.83 | 46 | DAN |
| 3 | 230 | 0.64 | 0.83 | 38 | DAN |
| 4 | 329 | 0.63 | 0.80 | 51 | empty |
| 5 | 323 | 0.59 | 0.78 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 153 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4YZ2 · Crystal Structure of Streptococcus pneumoniae NanC, in complex with… · 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 4YZ2 · PDBe 4YZ2 · UniProt Q97Q99
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