Research workbench
Crystal structure of streptococcus pneumoniae nanc, covalent complex with a fluorinated NEU5AC derivative
Analyse Crystal structure of streptococcus pneumoniae nanc, covalent complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F9T
- 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
- FSI, SFJ
- Pockets
- 15 · 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
- FSI · 5-acetamido-3,5-dideoxy-3-fluoro-D-erythro-alpha-L-manno-non-2-ulopyranosonic acid · ligand · 2 copies · chains A, B
- SFJ · (2R,3R,4R,5R,6R)-5-acetamido-2,3-difluoro-4-hydroxy-6-[(1R,2R)-1,2,3-trihydroxypropyl]tetrahydro-2H-pyran-2-carboxylic acid · ligand · 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
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 | 238 | 0.65 | 0.83 | 35 | FSI |
| 2 | 437 | 0.64 | 0.78 | 30 | empty |
| 3 | 294 | 0.63 | 0.80 | 33 | FSI |
| 4 | 307 | 0.56 | 0.76 | 26 | empty |
| 5 | 307 | 0.54 | 0.75 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 265 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5F9T · Crystal Structure of Streptococcus pneumoniae NanC, covalent complex with a fluorinated… · the same entry in another collection · chain B against B, 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 5F9T · PDBe 5F9T · UniProt A0A0H2UQE4
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