MolNFT v1 · #141530 · protein
Crystal structure of 3-hydroxypropionyl-CoA dehydratase from metallosphaera sedula
5ZAI · 3-hydroxypropionyl-coenzyme a dehydratase: “Crystal structure of 3-hydroxypropionyl-CoA dehydratase from metallosphaera sedula”. X-ray diffraction, 1 ligand (COA), 20 pockets (best druggability 0.75). MolNFT v1 #141530 on GenesisL1…
- PDB
- 5ZAI
- Type
- protein
- Length
- 1,545 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxypropionyl-coenzyme a dehydratase
- EC
- 4.2.1.116
- UniProt
- A4YI89
- Ligands
- COA
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 54% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F | 3-hydroxypropionyl-coenzyme a dehydratase (EC 4.2.1.116) | protein | 257 | 53% helix, 17% strand | A4YI89 |
| C | 3-hydroxypropionyl-coenzyme a dehydratase (EC 4.2.1.116) | protein | 259 | 54% helix, 17% strand | A4YI89 |
| D | 3-hydroxypropionyl-coenzyme a dehydratase (EC 4.2.1.116) | protein | 258 | 54% helix, 17% strand | A4YI89 |
Ligands and binding sites
- COA · Coenzyme A · ligand · 4 copies · chains A, C, B, D, E
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, C, D, F, E
- GOL · Glycerol · additive · 10 copies · chains A, C, B, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 148 | 0.75 | 0.93 | 37 | GOL |
| 2 | 105 | 0.69 | 0.92 | 28 | GOL |
| 3 | 217 | 0.65 | 0.83 | 43 | EDO |
| 4 | 285 | 0.63 | 0.80 | 43 | empty |
| 5 | 71 | 0.62 | 0.91 | 28 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2088 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 2084 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 2040 Ų buried · 32 hydrogen bonds · protein-protein
- D–E · 2026 Ų buried · 31 hydrogen bonds · protein-protein
- D–F · 2023 Ų buried · 29 hydrogen bonds · protein-protein
Compared structures
- 5ZAI · Crystal structure of 3-Hydroxypropionyl-CoA dehydratase from Metallosphaera sedula · the same entry in another collection · chain F against F, TM-score 1.00
- A4YI89 · AlphaFold monomer V2.0 prediction for 3-hydroxypropionyl-coenzyme a dehydratase (A4YI89) · 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 A4YI89
- Elsewhere: RCSB PDB 5ZAI · PDBe 5ZAI · UniProt A4YI89
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