Research workbench
Crystal structure of beta-ketoacyl-acp synthase III-2 (FABH2) (C113A) from vibrio cholerae co-crystallized with octanoyl-CoA
Analyse Crystal structure of beta-ketoacyl-acp synthase III-2 (FABH2) (C113A) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V0P
- Type
- protein
- Length
- 716 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
- CO8, NA
- Pockets
- 8 · best druggability 0.72
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-oxoacyl-[acyl-carrier-protein] synthase 3 protein 2 (EC 2.3.1.180) | protein | 358 | 40% helix, 23% strand | Q9KLJ3 |
Ligands and binding sites
- CO8 · Octanoyl-coenzyme A · ligand · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.72 | 0.89 | 31 | CO8 |
| 2 | 175 | 0.71 | 0.88 | 30 | CO8 |
| 3 | 139 | 0.46 | 0.77 | 20 | empty |
| 4 | 124 | 0.46 | 0.78 | 21 | empty |
| 5 | 92 | 0.37 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 3258 Ų buried · 67 hydrogen bonds · protein-protein
Compared structures
- 5V0P · Crystal Structure of Beta-ketoacyl-ACP synthase III-2 (FabH2) (C113A) from Vibrio… · 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 B 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 5V0P · PDBe 5V0P · UniProt Q9KLJ3
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