MolNFT v1 · #124773 · protein
Beta-ketoacyl-acp synthase III -2 (FABH2) (C113A) from vibrio cholerae cocrystallized with octanoyl-CoA: hydrolzed ligand
5KP2 · 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 2: “Beta-ketoacyl-acp synthase III -2 (FABH2) (C113A) from vibrio cholerae cocrystallized with octanoyl-CoA…”. X-ray diffraction, 2 ligands (COA, OCA), 7 pockets (best druggability…
- PDB
- 5KP2
- Type
- protein
- Length
- 715 residues
- Chains
- 2
- 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, OCA
- Pockets
- 7 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 2 (EC 2.3.1.180) | protein | 357 | 41% helix, 24% strand | Q9KLJ3 |
| B | 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
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 | 277 | 0.77 | 0.89 | 39 | OCA |
| 2 | 211 | 0.68 | 0.85 | 36 | empty |
| 3 | 184 | 0.55 | 0.79 | 19 | empty |
| 4 | 155 | 0.48 | 0.77 | 21 | empty |
| 5 | 96 | 0.36 | 0.74 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 3266 Ų buried · 68 hydrogen bonds · protein-protein
Compared structures
- 5KP2 · Beta-ketoacyl-ACP synthase III -2 (FabH2) (C113A) from Vibrio Cholerae cocrystallized… · the same entry in another collection · chain A against A, 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 1.00
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 5KP2 · PDBe 5KP2 · UniProt Q9KLJ3
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