MolNFT v1 · #73495 · protein
(R)-2-hydroxyisocaproyl-CoA dehydratase in complex with (R)-2- hydroxyisocaproate
3O3O · Alpha-subunit 2-hydroxyisocaproyl-CoA dehydratase: “(R)-2-hydroxyisocaproyl-CoA dehydratase in complex with (R)-2- hydroxyisocaproate”. X-ray diffraction, 3 ligands (SF4, 2RH, H2S), 13 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 3O3O
- Type
- protein
- Length
- 774 residues
- Chains
- 2
- 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, 2RH, H2S
- Pockets
- 13 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alpha-subunit 2-hydroxyisocaproyl-CoA dehydratase | protein | 399 | 58% helix, 10% strand | Q5U924 |
| B | Beta-subunit 2-hydroxyacyl-CoA dehydratase | protein | 375 | 54% helix, 12% strand | Q5U923 |
Ligands and binding sites
- SF4 · Iron/sulfur cluster · ligand · 2 copies · chains A, B
- 2RH · (2R)-2-hydroxy-4-methylpentanoic acid · ligand · chains A
- H2S · Hydrosulfuric acid · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 530 | 0.83 | 0.88 | 58 | SF4, 2RH |
| 2 | 163 | 0.80 | 0.96 | 34 | empty |
| 3 | 84 | 0.76 | 0.97 | 18 | SF4, H2S |
| 4 | 325 | 0.61 | 0.78 | 34 | empty |
| 5 | 78 | 0.61 | 0.90 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 2217 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 3O3O · (R)-2-hydroxyisocaproyl-CoA dehydratase in complex with (R)-2-hydroxyisocaproate · the same entry in another collection · chain A against A, 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 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 Q5U924
- Every structure of UniProt Q5U923
- Elsewhere: RCSB PDB 3O3O · PDBe 3O3O · UniProt Q5U924 · UniProt Q5U923
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