Research workbench
(R)-2-hydroxyisocaproyl-CoA dehydratase
Analyse (R)-2-hydroxyisocaproyl-CoA dehydratase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O3M
- Type
- protein
- Length
- 1,548 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha subunit 2-hydroxyisocaproyl-CoA dehydratase; Beta subunit 2-hydroxyacyl-CoA…
- UniProt
- Q5U924, Q5U923
- Ligands
- SF4, SO4, H2S
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 55% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha subunit 2-hydroxyisocaproyl-CoA dehydratase | protein | 399 | 57% helix, 11% strand | Q5U924 |
| B | Beta subunit 2-hydroxyacyl-CoA dehydratase | protein | 373 | 53% helix, 12% strand | Q5U923 |
| C | Alpha subunit 2-hydroxyisocaproyl-CoA dehydratase | protein | 401 | 57% helix, 10% strand | Q5U924 |
| D | Beta subunit 2-hydroxyacyl-CoA dehydratase | protein | 375 | 54% helix, 11% strand | Q5U923 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, C
- H2S · Hydrosulfuric acid · ion · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 475 | 0.81 | 0.88 | 61 | SF4, SO4 |
| 2 | 523 | 0.80 | 0.87 | 63 | SF4, SO4 |
| 3 | 127 | 0.79 | 0.97 | 34 | empty |
| 4 | 108 | 0.78 | 0.97 | 26 | empty |
| 5 | 73 | 0.76 | 0.98 | 20 | SF4, H2S |
Interfaces
3 interfaces between chains.
- A–B · 2215 Ų buried · 32 hydrogen bonds · protein-protein
- C–D · 2214 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 537 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 3O3M · (R)-2-Hydroxyisocaproyl-CoA Dehydratase · the same entry in another collection · chain D against D, TM-score 1.00
- Q5U923 · AlphaFold monomer V2.0 prediction for (R)-2-hydroxyisocaproyl-CoA dehydratase beta… · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q5U924 · AlphaFold monomer V2.0 prediction for (R)-2-hydroxyisocaproyl-CoA dehydratase alpha… · a predicted model of the same protein · chain C 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 Q5U924
- Every structure of UniProt Q5U923
- Elsewhere: RCSB PDB 3O3M · PDBe 3O3M · UniProt Q5U924 · UniProt Q5U923
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