Research workbench
Crosslinked crystal structure of type II fatty acid synthase ketosynthase, fabf, and C16-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
- 6OKG
- Type
- protein
- Length
- 488 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier-protein] synthase 2; Acyl carrier protein
- EC
- 2.3.1.179
- UniProt
- P0AAI5, P0A6A8
- Ligands
- MU4, NA
- Pockets
- 4 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 (EC 2.3.1.179) | protein | 411 | 38% helix, 21% strand | P0AAI5 |
| B | Acyl carrier protein | protein | 77 | 53% helix, 3% strand | P0A6A8 |
Ligands and binding sites
- MU4 · N-[2-(hexadecanoylamino)ethyl]-N~3~-[(2R)-2-hydroxy-3, 3-dimethyl-4-(phosphonooxy)butanoyl]-beta-alaninamide · ligand · chains A, B
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 274 | 0.61 | 0.79 | 39 | MU4 |
| 2 | 56 | 0.38 | 0.80 | 14 | empty |
| 3 | 83 | 0.35 | 0.75 | 16 | empty |
| 4 | 83 | 0.30 | 0.73 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 206 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6OKG · Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabF, and… · the same entry in another collection · chain A against A, TM-score 1.00
- P0AAI5 · AlphaFold monomer V2.0 prediction for 3-oxoacyl-[acyl-carrier- protein] synthase 2… · a predicted model of the same protein · chain A against A, TM-score 0.99
- P0A6A8 · AlphaFold monomer V2.0 prediction for acyl carrier protein (P0A6A8) · a predicted model of the same protein · chain B 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 P0AAI5
- Every structure of UniProt P0A6A8
- Elsewhere: RCSB PDB 6OKG · PDBe 6OKG · UniProt P0AAI5 · UniProt P0A6A8
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