MolNFT v1 · #123250 · protein
The crystal structure of bacillus cereus 3-hydroxyisobutyrate dehydrogenase in complex with NAD
5JE8: “The crystal structure of bacillus cereus 3-hydroxyisobutyrate dehydrogenase in complex with NAD”. X-ray diffraction, 1 ligand (NAD), 5 pockets (best druggability 0.84). MolNFT v1 #123250 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5JE8
- Type
- protein
- Length
- 1,166 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
- Q81DR6
- Ligands
- NAD
- Pockets
- 5 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 57% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) | protein | 291 | 56% helix, 14% strand | Q81DR6 |
| B | 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) | protein | 294 | 56% helix, 15% strand | Q81DR6 |
| C | 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) | protein | 289 | 57% helix, 14% strand | Q81DR6 |
| D | 3-hydroxyisobutyrate dehydrogenase (EC 1.1.1.31) | protein | 292 | 57% helix, 14% strand | Q81DR6 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 4 copies · chains A, B, D, C
- GOL · Glycerol · additive · 2 copies · chains B, D
- EPE · 4-(2-hydroxyethyl)-1-piperazine ethanesulfonic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1046 | 0.84 | 0.84 | 101 | GOL, NAD |
| 2 | 596 | 0.82 | 0.87 | 68 | NAD |
| 3 | 474 | 0.70 | 0.80 | 59 | NAD, EPE |
| 4 | 447 | 0.68 | 0.80 | 49 | NAD |
| 5 | 58 | 0.28 | 0.74 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2753 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2624 Ų buried · 33 hydrogen bonds · protein-protein
- B–D · 1053 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 72 Ų buried · 0 hydrogen bonds · protein-protein
- A–D · 63 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5JE8 · The crystal structure of Bacillus cereus 3-hydroxyisobutyrate dehydrogenase in complex… · the same entry in another collection · chain A 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 Q81DR6
- Elsewhere: RCSB PDB 5JE8 · PDBe 5JE8 · UniProt Q81DR6
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