Research workbench
Mycobacterium tuberculosis 3-hydroxyisobutyrate dehydrogenase (mthibadh) + (S)-3-hydroxyisobutyrate (S-hiba)
Analyse Mycobacterium tuberculosis 3-hydroxyisobutyrate dehydrogenase (mthibadh) +… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5Y8I
- Type
- protein
- Length
- 583 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable 3-hydroxyisobutyrate dehydrogenase
- EC
- 1.1.1.31
- UniProt
- P9WNY5
- Ligands
- 9ON, HUI
- Pockets
- 3 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 55% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Probable 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) | protein | 292 | 55% helix, 14% strand | P9WNY5 |
| B | Probable 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) | protein | 291 | 55% helix, 14% strand | P9WNY5 |
Ligands and binding sites
- 9ON · (2~{S})-2-methylpentanedioic acid · ligand · 2 copies · chains A, B
- HUI · (2S)-2-methyl-3-oxidanyl-propanoic acid · ligand · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 398 | 0.64 | 0.78 | 52 | HUI |
| 2 | 397 | 0.63 | 0.78 | 49 | empty |
| 3 | 54 | 0.32 | 0.77 | 14 | GOL |
Interfaces
1 interface between chains.
- A–B · 2298 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5Y8I · Mycobacterium tuberculosis 3-Hydroxyisobutyrate dehydrogenase (MtHIBADH) +… · the same entry in another collection · chain A against A, TM-score 1.00
- P9WNY5 · AlphaFold monomer V2.0 prediction for probable 3-hydroxyisobutyrate dehydrogenase (P9WNY5) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 P9WNY5
- Elsewhere: RCSB PDB 5Y8I · PDBe 5Y8I · UniProt P9WNY5
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