Research workbench
Crosslinked crystal structure of type II fatty acid synthase ketosynthase, fabb, 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
- 6OKF
- Type
- protein
- Length
- 962 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier-protein] synthase 1; Acyl carrier protein
- EC
- 2.3.1.41
- UniProt
- P0A953, P0A6A8
- Ligands
- MRJ, NA
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 41% 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, 23% strand | P0A953 |
| C, D | Acyl carrier protein | protein | 77 | 56% 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
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 526 | 0.77 | 0.84 | 75 | MRJ |
| 2 | 331 | 0.77 | 0.87 | 46 | MRJ |
| 3 | 250 | 0.58 | 0.79 | 31 | empty |
| 4 | 66 | 0.35 | 0.77 | 17 | empty |
| 5 | 98 | 0.35 | 0.74 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2942 Ų buried · 48 hydrogen bonds · protein-protein
- B–D · 525 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 520 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 154 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 140 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6OKF · 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 A 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 0.96
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 6OKF · PDBe 6OKF · UniProt P0A953 · UniProt P0A6A8
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