Research workbench
Crystal structure of beta-hydroxyacyl-acyl carrier protein dehydratase (fabz) from yersinia pestis
Analyse Crystal structure of beta-hydroxyacyl-acyl carrier protein dehydratase (fabz)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5BUW
- Type
- protein
- Length
- 288 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
- Q8ZH57
- Ligands
- SCN
- Pockets
- 7 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 22% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | 3-hydroxyacyl-[acyl-carrier-protein] dehydratase fabz (EC 4.2.1.59) | protein | 144 | 22% helix, 40% strand | Q8ZH57 |
Ligands and binding sites
- SCN · Thiocyanate ion · ion · 4 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.65 | 0.90 | 26 | SCN, EDO |
| 2 | 77 | 0.63 | 0.90 | 24 | EDO, SCN |
| 3 | 84 | 0.42 | 0.79 | 20 | SCN |
| 4 | 72 | 0.42 | 0.80 | 16 | empty |
| 5 | 56 | 0.31 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1431 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 5BUW · Crystal Structure of beta-hydroxyacyl-acyl carrier protein dehydratase (FabZ) from… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZH57 · AlphaFold monomer V2.0 prediction for 3-hydroxyacyl-[acyl-carrier- protein] dehydratase… · a predicted model of the same protein · chain B 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 Q8ZH57
- Elsewhere: RCSB PDB 5BUW · PDBe 5BUW · UniProt Q8ZH57
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