Research workbench
Crystal structure of beta-ketoacyl-acp synthase III (fabh) from vibrio cholerae in complex with coenzyme a
Analyse Crystal structure of beta-ketoacyl-acp synthase III (fabh) 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
- 4NHD
- Type
- protein
- Length
- 1,269 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 1
- EC
- 2.3.1.180
- UniProt
- Q9KQH5
- Ligands
- COA, CA, NA
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 1 (EC 2.3.1.180) | protein | 317 | 40% helix, 28% strand | Q9KQH5 |
| D | 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 1 (EC 2.3.1.180) | protein | 318 | 40% helix, 28% strand | Q9KQH5 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 7 copies · chains A, B, C, D
- NA · Sodium ion · metal · 3 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 495 | 0.79 | 0.86 | 52 | empty |
| 2 | 630 | 0.78 | 0.84 | 62 | empty |
| 3 | 940 | 0.74 | 0.77 | 69 | CA |
| 4 | 229 | 0.70 | 0.86 | 35 | COA |
| 5 | 208 | 0.70 | 0.86 | 29 | COA |
Interfaces
3 interfaces between chains.
- A–C · 2437 Ų buried · 48 hydrogen bonds · protein-protein
- B–D · 2432 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 229 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (acetylation).
Compared structures
- 4NHD · Crystal structure of beta-ketoacyl-ACP synthase III (FabH) from Vibrio Cholerae in… · the same entry in another collection · chain D against D, TM-score 1.00
- Q9KQH5 · AlphaFold monomer V2.0 prediction for 3-oxoacyl-[acyl-carrier- protein] synthase 3… · a predicted model of the same protein · chain C 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 Q9KQH5
- Elsewhere: RCSB PDB 4NHD · PDBe 4NHD · UniProt Q9KQH5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.