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Crystal structure of beta-ketoacyl-acp synthase II (fabf) from vibrio cholerae (space group P43) at 2.2 ångström
Analyse Crystal structure of beta-ketoacyl-acp synthase II (fabf) from vibrio cholerae… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JRH
- Type
- protein
- Length
- 825 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier-protein] synthase 2
- EC
- 2.3.1.179
- UniProt
- Q9KQH9
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-oxoacyl-[acyl-carrier-protein] synthase 2 (EC 2.3.1.179) | protein | 412 | 40% helix, 22% strand | Q9KQH9 |
| B | 3-oxoacyl-[acyl-carrier-protein] synthase 2 (EC 2.3.1.179) | protein | 413 | 40% helix, 22% strand | Q9KQH9 |
Ligands and binding sites
- ACT · Acetate ion · additive · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.76 | 0.98 | 29 | empty |
| 2 | 227 | 0.70 | 0.86 | 44 | empty |
| 3 | 218 | 0.70 | 0.86 | 43 | empty |
| 4 | 114 | 0.53 | 0.82 | 26 | ACT |
| 5 | 62 | 0.40 | 0.80 | 14 | ACT |
Interfaces
1 interface between chains.
- A–B · 3028 Ų buried · 31 hydrogen bonds · protein-protein
Compared structures
- 4JRH · Crystal structure of beta-ketoacyl-ACP synthase II (FabF) from Vibrio Cholerae (space… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9KQH9 · 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 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 Q9KQH9
- Elsewhere: RCSB PDB 4JRH · PDBe 4JRH · UniProt Q9KQH9
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