Crosslinked crystal structure of type II fatty acid synthase ketosynthase, fabf, and C8-crypto acyl carrier protein, acpp

Structure

x-ray diffraction · 3 distinct chains · 41% helix, 20% strand (DSSP).

Ligands and binding sites

• DYF · [(3~{R})-2,2-dimethyl-4-[[3-[2-[[(~{E})-oct-2-enoyl]amino]ethylamino]-3-oxidanylidene-propyl]amino]-3-oxidanyl-4-oxidanylidene-butyl] dihydrogen phosphate · ligand · 2 copies · chains A, B, C, D
• 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

11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Interfaces

5 interfaces between chains.

• A–B · 3021 Ų buried · 24 hydrogen bonds · protein-protein
• B–D · 562 Ų buried · 11 hydrogen bonds · protein-protein
• A–C · 481 Ų buried · 6 hydrogen bonds · protein-protein
• A–D · 254 Ų buried · 2 hydrogen bonds · protein-protein
• B–C · 235 Ų buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 covalent (covalent ligand).

Compared structures

• 7L4L · Crosslinked Crystal Structure of Type II Fatty Acid Synthase Ketosynthase, FabF, and… · the same entry in another collection · chain D against D, 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 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 0.98

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 7L4L · PDBe 7L4L · UniProt P0AAI5 · UniProt P0A6A8