Research workbench
Crystal structure of L-2-hydroxyisocaproate dehydrogenase from lactobacillus confusus at 2.2 ångströms resolution-an example of strong asymmetry between subunits
Analyse Crystal structure of L-2-hydroxyisocaproate dehydrogenase from lactobacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HYH
- Type
- protein
- Length
- 1,185 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- L-2-hydroxyisocaproate dehydrogenase
- EC
- 1.1.1.27
- UniProt
- P14295
- Ligands
- NAD, SO4
- Pockets
- 14 · best druggability 0.90
Structure
x-ray diffraction · 3 distinct chains · 51% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | L-2-hydroxyisocaproate dehydrogenase (EC 1.1.1.27) | protein | 297 | 49% helix, 19% strand | P14295 |
| B | L-2-hydroxyisocaproate dehydrogenase (EC 1.1.1.27) | protein | 294 | 50% helix, 19% strand | P14295 |
| C, D | L-2-hydroxyisocaproate dehydrogenase (EC 1.1.1.27) | protein | 297 | 53% helix, 19% strand | P14295 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.90 | 0.92 | 151 | empty |
| 2 | 429 | 0.73 | 0.83 | 49 | SO4, NAD |
| 3 | 436 | 0.71 | 0.81 | 51 | SO4, NAD |
| 4 | 113 | 0.61 | 0.86 | 19 | empty |
| 5 | 109 | 0.60 | 0.86 | 22 | empty |
Interfaces
6 interfaces between chains.
- B–D · 2165 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 2154 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 885 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 865 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 587 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 1HYH · Crystal structure of L-2-hydroxyisocaproate dehydrogenase from lactobacillus confusus at… · the same entry in another collection · chain D against D, TM-score 1.00
- P14295 · AlphaFold monomer V2.0 prediction for L-2-hydroxyisocaproate dehydrogenase (P14295) · 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 P14295
- Elsewhere: RCSB PDB 1HYH · PDBe 1HYH · UniProt P14295
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