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High resolution structure of 3-hydroxydecanoyl-(acyl carrier protein) dehydratase from yersinia pestis at 1.35 a
Analyse High resolution structure of 3-hydroxydecanoyl-(acyl carrier protein)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5HD6
- Type
- protein
- Length
- 1,381 residues
- Chains
- 8
- 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
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 20% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.59) | protein | 175 | 19% helix, 36% strand | A0A0B6NZG1 |
| E | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.59) | protein | 173 | 20% helix, 36% strand | A0A0B6NZG1 |
| F, G | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.59) | protein | 168 | 20% helix, 37% strand | A0A0B6NZG1 |
| H | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.59) | protein | 172 | 20% helix, 36% strand | A0A0B6NZG1 |
Ligands and binding sites
- GOL · Glycerol · additive · 15 copies · chains A, G, B, F, C, E, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.79 | 0.98 | 28 | GOL |
| 2 | 108 | 0.79 | 0.98 | 26 | GOL |
| 3 | 103 | 0.78 | 0.98 | 28 | GOL |
| 4 | 105 | 0.78 | 0.98 | 27 | GOL |
| 5 | 81 | 0.75 | 0.98 | 26 | GOL |
Interfaces
10 interfaces between chains.
- D–H · 1655 Ų buried · 29 hydrogen bonds · protein-protein
- B–F · 1639 Ų buried · 29 hydrogen bonds · protein-protein
- C–E · 1628 Ų buried · 29 hydrogen bonds · protein-protein
- A–G · 1609 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 324 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 70 modified (engineered).
Compared structures
- 5HD6 · High resolution 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 5HD6 · PDBe 5HD6 · UniProt A0A0B6NZG1
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