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Beta-ketoacyl-(acyl carrier protein) synthase III-2 (FABH2) from vibrio cholerae soaked with acetyl-CoA
Analyse Beta-ketoacyl-(acyl carrier protein) synthase III-2 (FABH2) from vibrio… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X0O
- Type
- protein
- Length
- 2,872 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 2
- EC
- 2.3.1.180
- UniProt
- Q9KLJ3
- Ligands
- COA, NA
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, F, G | 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 2 (EC 2.3.1.180) | protein | 359 | 42% helix, 24% strand | Q9KLJ3 |
| E | 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 2 (EC 2.3.1.180) | protein | 360 | 41% helix, 24% strand | Q9KLJ3 |
| H | 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 2 (EC 2.3.1.180) | protein | 358 | 41% helix, 24% strand | Q9KLJ3 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 7 copies · chains A, B, D, E, F, G, H
- NA · Sodium ion · metal · 7 copies · chains A, B, C, D, F, G, H
- MLI · Malonate ion · additive · chains E, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 164 | 0.68 | 0.87 | 32 | empty |
| 2 | 134 | 0.66 | 0.87 | 27 | empty |
| 3 | 121 | 0.60 | 0.85 | 23 | empty |
| 4 | 112 | 0.57 | 0.84 | 22 | empty |
| 5 | 102 | 0.56 | 0.84 | 23 | empty |
Interfaces
6 interfaces between chains.
- E–G · 3253 Ų buried · 65 hydrogen bonds · protein-protein
- F–H · 3242 Ų buried · 68 hydrogen bonds · protein-protein
- A–C · 3242 Ų buried · 66 hydrogen bonds · protein-protein
- B–D · 3207 Ų buried · 67 hydrogen bonds · protein-protein
- D–F · 572 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 modified (acetylation).
Compared structures
- 4X0O · Beta-ketoacyl-(acyl carrier protein) synthase III-2 (FabH2) from Vibrio cholerae soaked… · the same entry in another collection · chain H against H, TM-score 1.00
- Q9KLJ3 · 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 Q9KLJ3
- Elsewhere: RCSB PDB 4X0O · PDBe 4X0O · UniProt Q9KLJ3
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