MolNFT v1 · #142990 · protein
The crystal structure of the staphylococcus aureus fatty acid kinase (fak) B1 protein loaded with 12-methyl myristic acid (C15:0) to 1.63 ångström resolution
6ALW · Edd domain protein, degv family: “The crystal structure of the staphylococcus aureus fatty acid kinase (fak) B1 protein loaded with 12-methyl…”. X-ray diffraction, 2 ligands (BNV, BMJ), 8 pockets (best druggability 0.78). MolNFT v1…
- PDB
- 6ALW
- Type
- protein
- Length
- 569 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Edd domain protein, degv family
- UniProt
- X5EH37
- Ligands
- BNV, BMJ
- Pockets
- 8 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Edd domain protein, degv family | protein | 288 | 40% helix, 24% strand | X5EH37 |
| B | Edd domain protein, degv family | protein | 281 | 41% helix, 24% strand | X5EH37 |
Ligands and binding sites
- BNV · (12S)-12-methyltetradecanoic acid · ligand · 2 copies · chains A, B
- BMJ · (12R)-12-methyltetradecanoic acid · ligand · 2 copies · chains A, B
- GOL · Glycerol · additive · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 139 | 0.78 | 0.95 | 29 | BNV, BMJ |
| 2 | 796 | 0.76 | 0.80 | 105 | BNV, BMJ |
| 3 | 177 | 0.53 | 0.78 | 29 | empty |
| 4 | 201 | 0.53 | 0.77 | 32 | GOL |
| 5 | 73 | 0.38 | 0.78 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 509 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6ALW · The crystal structure of the Staphylococcus aureus Fatty acid Kinase (Fak) B1 protein… · 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 6ALW · PDBe 6ALW · UniProt X5EH37
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