Research workbench
Crystal structure of 3-hydroxydecanoyl-(acyl carrier protein) dehydratase from yersinia pestis
Analyse Crystal structure of 3-hydroxydecanoyl-(acyl carrier protein) dehydratase from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q62
- Type
- protein
- Length
- 341 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase
- EC
- 4.2.1.60
- UniProt
- Q66CF3
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.60) | protein | 170 | 20% helix, 35% strand | Q66CF3 |
| B | 3-hydroxydecanoyl-[acyl-carrier-protein] dehydratase (EC 4.2.1.60) | protein | 171 | 20% helix, 36% strand | Q66CF3 |
Ligands and binding sites
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.67 | 0.91 | 29 | MES |
| 2 | 113 | 0.66 | 0.89 | 29 | MES |
Interfaces
1 interface between chains.
- A–B · 1462 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 3Q62 · Crystal Structure of 3-hydroxydecanoyl-(acyl carrier protein) dehydratase from Yersinia… · the same entry in another collection · chain A against A, TM-score 1.00
- Q66CF3 · AlphaFold monomer V2.0 prediction for 3-hydroxydecanoyl-[acyl- carrier-protein]… · a predicted model of the same protein · chain A against A, TM-score 0.97
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 Q66CF3
- Elsewhere: RCSB PDB 3Q62 · PDBe 3Q62 · UniProt Q66CF3
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