Research workbench
The X-ray crystal structure of the streptococcus pneumoniae fatty acid kinase (fak) B3 protein loaded with linoleic acid to 1.47 ångström resolution
Analyse The X-ray crystal structure of the streptococcus pneumoniae fatty acid kinase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CNG
- Type
- protein
- Length
- 562 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fatty acid kinase (fak) B3 protein
- UniProt
- Q8DQI6
- Ligands
- EIC, NA
- Pockets
- 3 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Fatty acid kinase (fak) B3 protein | protein | 281 | 38% helix, 28% strand | Q8DQI6 |
Ligands and binding sites
- EIC · Linoleic acid · ligand · 2 copies · chains A, D
- NA · Sodium ion · metal · 2 copies · chains A, D
- GOL · Glycerol · additive · 13 copies · chains A, D
- ACT · Acetate ion · additive · 5 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.85 | 0.88 | 99 | EIC |
| 2 | 89 | 0.40 | 0.78 | 20 | NA |
| 3 | 70 | 0.35 | 0.77 | 21 | NA, GOL |
Interfaces
1 interface between chains.
- A–D · 1046 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 6CNG · The X-ray crystal structure of the Streptococcus pneumoniae Fatty Acid Kinase (Fak) B3… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8DQI6 · AlphaFold monomer V2.0 prediction for degv domain-containing protein SPR0652 (Q8DQI6) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8DQI6
- Elsewhere: RCSB PDB 6CNG · PDBe 6CNG · UniProt Q8DQI6
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