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Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabB, and C12-crypto Acyl Carrier Protein, AcpP
Analyse Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OKC
- Type
- protein
- Length
- 962 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.55
- Source
- Escherichia coli (strain K12)
- Molecule
- 3-oxoacyl-[acyl-carrier-protein] synthase 1; Acyl carrier protein
- EC
- 2.3.1.41
- UniProt
- P0A953, P0A6A8
- Ligands
- MRJ
- Pockets
- 6 · best druggability 0.79
Structure
x-ray diffraction · resolution 1.55 · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-oxoacyl-[acyl-carrier-protein] synthase 1 (EC 2.3.1.41) | protein | 404 | 38% helix, 22% strand | P0A953 |
| C, D | Acyl carrier protein | protein | 77 | 55% helix, 3% strand | P0A6A8 |
Ligands and binding sites
- MRJ · N-[2-(dodecanoylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3,3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide · ligand · 2 copies · chains A, B, D, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 703 | 0.79 | 0.84 | 86 | MRJ |
| 2 | 587 | 0.78 | 0.84 | 79 | MRJ |
| 3 | 122 | 0.44 | 0.77 | 28 | empty |
| 4 | 131 | 0.44 | 0.76 | 30 | empty |
| 5 | 89 | 0.33 | 0.74 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2982 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 521 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 518 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 161 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 139 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6OKC · Crosslinked crystal structure of type II fatty acid synthase ketosynthase, fabb, and… · the same entry in another collection · chain D against D, TM-score 1.00
- P0A953 · AlphaFold monomer V2.0 prediction for 3-oxoacyl-[acyl-carrier- protein] synthase 1… · a predicted model of the same protein · chain B against A, TM-score 1.00
- P0A6A8 · AlphaFold monomer V2.0 prediction for acyl carrier protein (P0A6A8) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 P0A953
- Every structure of UniProt P0A6A8
- Elsewhere: RCSB PDB 6OKC · PDBe 6OKC · UniProt P0A953 · UniProt P0A6A8
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