Research workbench
Staphylococcus aureus fabh with covalent inhibitor OXA1
Analyse Staphylococcus aureus fabh with covalent inhibitor OXA1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KVS
- Type
- protein
- Length
- 626 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier-protein] synthase 3
- EC
- 2.3.1.180
- UniProt
- A7X0K2
- Ligands
- OAX
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-oxoacyl-[acyl-carrier-protein] synthase 3 (EC 2.3.1.180) | protein | 313 | 42% helix, 27% strand | A7X0K2 |
Ligands and binding sites
- OAX · 4-chloranyl-N-[[cyclopropylmethyl(methanoyl) amino]methyl]benzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.73 | 0.89 | 36 | OAX |
| 2 | 245 | 0.71 | 0.85 | 33 | OAX |
| 3 | 475 | 0.69 | 0.79 | 36 | empty |
| 4 | 69 | 0.28 | 0.72 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 2007 Ų buried · 30 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6KVS · Staphylococcus aureus FabH with covalent inhibitor Oxa1 · the same entry in another collection · chain A against A, TM-score 1.00
- A7X0K2 · AlphaFold monomer V2.0 prediction for 3-oxoacyl-[acyl-carrier- protein] synthase 3… · 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 A7X0K2
- Elsewhere: RCSB PDB 6KVS · PDBe 6KVS · UniProt A7X0K2
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