Research workbench
Crystal structure of human hydroxyisobutyrate dehydrogenase complexed with NAD+
Analyse Crystal structure of human hydroxyisobutyrate dehydrogenase complexed with NAD+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2I9P
- Type
- protein
- Length
- 1,175 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-hydroxyisobutyrate dehydrogenase
- EC
- 1.1.1.31
- UniProt
- P31937
- Ligands
- NAD
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) | protein | 293 | 52% helix, 14% strand | P31937 |
| B | 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) | protein | 296 | 52% helix, 14% strand | P31937 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.66 | 0.79 | 54 | NAD |
| 2 | 396 | 0.66 | 0.79 | 53 | NAD |
| 3 | 375 | 0.64 | 0.79 | 54 | NAD |
| 4 | 336 | 0.64 | 0.79 | 36 | NAD |
| 5 | 335 | 0.54 | 0.74 | 47 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2530 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2498 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 715 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 708 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 446 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2I9P · Crystal structure of human hydroxyisobutyrate dehydrogenase complexed with NAD+ · the same entry in another collection · chain D against D, TM-score 1.00
- P31937 · AlphaFold monomer V2.0 prediction for 3-hydroxyisobutyrate dehydrogenase, mitochondrial… · a predicted model of the same protein · chain D against A, TM-score 1.00
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 P31937
- Elsewhere: RCSB PDB 2I9P · PDBe 2I9P · UniProt P31937
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