Research workbench
Crystal structure of 3-oxoacyl-(acyl carrier protein) synthase III from rhodopseudomonas palustris CGA009
Analyse Crystal structure of 3-oxoacyl-(acyl carrier protein) synthase III from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3LED
- Type
- protein
- Length
- 750 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-oxoacyl-acyl carrier protein synthase III
- EC
- 2.3.1.41
- UniProt
- Q6NA87
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-oxoacyl-acyl carrier protein synthase III (EC 2.3.1.41) | protein | 375 | 40% helix, 24% strand | Q6NA87 |
Ligands and binding sites
- FMT · Formic acid · additive · 2 copies · chains 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.80 | 0.89 | 48 | empty |
| 2 | 73 | 0.64 | 0.92 | 20 | empty |
| 3 | 175 | 0.63 | 0.84 | 28 | FMT |
| 4 | 454 | 0.63 | 0.77 | 55 | empty |
| 5 | 148 | 0.63 | 0.85 | 26 | empty |
Interfaces
1 interface between chains.
- A–B · 3516 Ų buried · 58 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 modified (engineered).
Compared structures
- 3LED · Crystal structure of 3-oxoacyl-(acyl carrier protein) synthase III from Rhodopseudomonas… · the same entry in another collection · 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 Q6NA87
- Elsewhere: RCSB PDB 3LED · PDBe 3LED · UniProt Q6NA87
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