MolNFT v1 · #118591 · protein
Co-crystal structure of 3-hydroxydecanoyl-(acyl carrier protein) dehydratase from yersinia pestis with 5-benzoylpentanoic acid
5F6R · 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase: “Co-crystal structure of 3-hydroxydecanoyl-(acyl carrier protein) dehydratase from yersinia pestis with…”. X-ray diffraction, 2 ligands (5VO, PO4), 3 pockets (best druggability…
- PDB
- 5F6R
- Type
- protein
- Length
- 345 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
- UniProt
- A0A0B6NZG1
- Ligands
- 5VO, PO4
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.59) | protein | 173 | 20% helix, 35% strand | A0A0B6NZG1 |
| B | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.59) | protein | 172 | 20% helix, 35% strand | A0A0B6NZG1 |
Ligands and binding sites
- 5VO · 6-oxidanylidene-6-phenyl-hexanoic acid · ligand · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 138 | 0.68 | 0.89 | 32 | 5VO |
| 2 | 119 | 0.66 | 0.89 | 31 | 5VO |
| 3 | 50 | 0.29 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 1460 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 5F6R · Co-crystal Structure of 3-hydroxydecanoyl-(acyl carrier protein) Dehydratase from… · 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 A0A0B6NZG1
- Elsewhere: RCSB PDB 5F6R · PDBe 5F6R · UniProt A0A0B6NZG1
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