MolNFT v1 · #158594 · protein
The X-ray crystal structure of staphylococcus aureus fatty acid kinase (fak) B1 F263T mutant protein to 2.18 ångström resolution
6NYU · Degv domain-containing protein: “The X-ray crystal structure of staphylococcus aureus fatty acid kinase (fak) B1 F263T mutant protein to 2.18…”. X-ray diffraction, 2 ligands (MYR, PLM), 6 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 6NYU
- Type
- protein
- Length
- 563 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Degv domain-containing protein
- UniProt
- X5EH37
- Ligands
- MYR, PLM
- Pockets
- 6 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Degv domain-containing protein | protein | 283 | 41% helix, 24% strand | X5EH37 |
| B | Degv domain-containing protein | protein | 280 | 41% helix, 24% strand | X5EH37 |
Ligands and binding sites
- MYR · Myristic acid · ligand · 2 copies · chains A, B
- PLM · Palmitic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.80 | 0.96 | 34 | MYR, PLM |
| 2 | 584 | 0.75 | 0.82 | 93 | MYR, PLM |
| 3 | 192 | 0.54 | 0.78 | 29 | empty |
| 4 | 216 | 0.54 | 0.77 | 35 | empty |
| 5 | 55 | 0.33 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 449 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 6NYU · The X-ray crystal structure of Staphylococcus aureus Fatty Acid Kinase (Fak) B1 F263T… · 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 X5EH37
- Elsewhere: RCSB PDB 6NYU · PDBe 6NYU · UniProt X5EH37
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