MolNFT v1 · #143708 · protein
The crystal structure of 3-hydroxydecanoyl-(acyl carrier protein) dehydratase from vibrio cholerae O1 biovar eltor str. N16961
6B7J · 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase: “The crystal structure of 3-hydroxydecanoyl-(acyl carrier protein) dehydratase from vibrio cholerae O1 biovar…”. X-ray diffraction, 4 pockets (best druggability 0.79). MolNFT v1…
- PDB
- 6B7J
- Type
- protein
- Length
- 347 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
- EC
- 4.2.1.59, 5.3.3.14
- UniProt
- A5F850
- Pockets
- 4 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.59, 5.3.3.14) | protein | 174 | 18% helix, 36% strand | A5F850 |
| B | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.59, 5.3.3.14) | protein | 173 | 18% helix, 36% strand | A5F850 |
Ligands and binding sites
- FMT · Formic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 104 | 0.79 | 0.98 | 28 | empty |
| 2 | 98 | 0.77 | 0.98 | 28 | empty |
| 3 | 56 | 0.38 | 0.80 | 12 | FMT |
| 4 | 54 | 0.37 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1625 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 6B7J · The crystal structure of 3-hydroxydecanoyl-(acyl carrier protein) dehydratase from Vibrio… · the same entry in another collection · chain A against A, TM-score 1.00
- A5F850 · AlphaFold monomer V2.0 prediction for 3-hydroxydecanoyl-[acyl- carrier-protein]… · a predicted model of the same protein · chain B against A, TM-score 0.98
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 A5F850
- Elsewhere: RCSB PDB 6B7J · PDBe 6B7J · UniProt A5F850
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