MolNFT v1 · #114614 · protein
Crystal structure of 3-hydroxyacyl-acp dehydratase (fabz) from yersinia pestis with glycerol bound
5BUX · 3-hydroxyacyl-[acyl-carrier-protein] dehydratase fabz: “Crystal structure of 3-hydroxyacyl-acp dehydratase (fabz) from yersinia pestis with glycerol bound”. X-ray diffraction, 1 ligand (SCN), 6 pockets (best druggability 0.74).…
- PDB
- 5BUX
- Type
- protein
- Length
- 285 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxyacyl-[acyl-carrier-protein] dehydratase fabz
- EC
- 4.2.1.59
- UniProt
- Q1CAM3
- Ligands
- SCN
- Pockets
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 22% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-hydroxyacyl-[acyl-carrier-protein] dehydratase fabz (EC 4.2.1.59) | protein | 142 | 23% helix, 40% strand | Q1CAM3 |
| B | 3-hydroxyacyl-[acyl-carrier-protein] dehydratase fabz (EC 4.2.1.59) | protein | 143 | 22% helix, 40% strand | Q1CAM3 |
Ligands and binding sites
- SCN · Thiocyanate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 197 | 0.74 | 0.89 | 31 | GOL |
| 2 | 208 | 0.71 | 0.87 | 32 | GOL |
| 3 | 105 | 0.54 | 0.83 | 25 | SCN |
| 4 | 57 | 0.39 | 0.80 | 13 | empty |
| 5 | 60 | 0.37 | 0.79 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1294 Ų buried · 19 hydrogen bonds · protein-protein
Compared structures
- Q1CAM3 · AlphaFold monomer V2.0 prediction for 3-hydroxyacyl-[acyl-carrier- protein] dehydratase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q1CAM3
- Elsewhere: RCSB PDB 5BUX · PDBe 5BUX · UniProt Q1CAM3
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