MolNFT v1 · #96709 · protein
Crystal structure of beta-ketoacyl-acp synthase II (fabf) from vibrio cholerae (space group P212121) at 1.75 ångström
4JRM · 3-oxoacyl-[acyl-carrier-protein] synthase 2: “Crystal structure of beta-ketoacyl-acp synthase II (fabf) from vibrio cholerae (space group P212121) at 1.75…”. X-ray diffraction, 16 pockets (best druggability 0.76). MolNFT v1 #96709…
- PDB
- 4JRM
- Type
- protein
- Length
- 1,649 residues
- Chains
- 4
- 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
- 16 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, B | 3-oxoacyl-[acyl-carrier-protein] synthase 2 (EC 2.3.1.179) | protein | 412 | 40% helix, 22% strand | Q9KQH9 |
| C | 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 D, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 76 | 0.76 | 0.98 | 30 | empty |
| 2 | 71 | 0.75 | 0.99 | 31 | empty |
| 3 | 785 | 0.74 | 0.79 | 80 | empty |
| 4 | 235 | 0.70 | 0.86 | 45 | empty |
| 5 | 211 | 0.69 | 0.86 | 46 | empty |
Interfaces
5 interfaces between chains.
- D–C · 3031 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2932 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 570 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 439 Ų buried · 9 hydrogen bonds · protein-protein
- D–A · 38 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4JRM · Crystal structure of beta-ketoacyl-ACP synthase II (FabF) from Vibrio Cholerae (space… · the same entry in another collection · chain C against C, 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 4JRM · PDBe 4JRM · UniProt Q9KQH9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.