MolNFT v1 · #109171 · protein
Structure of the E270A mutant isopropylmalate dehydrogenase from thermus thermophilus in complex with ipm, mn and NADH
4WUO · 3-isopropylmalate dehydrogenase: “Structure of the E270A mutant isopropylmalate dehydrogenase from thermus thermophilus in complex with ipm, mn…”. X-ray diffraction, 4 ligands (IPM, NAD, MN), 7 pockets (best druggability 0.78).…
- PDB
- 4WUO
- Type
- protein
- Length
- 694 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 3-isopropylmalate dehydrogenase
- EC
- 1.1.1.85
- UniProt
- Q5SIY4
- Ligands
- IPM, NAD, MN, K
- Pockets
- 7 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 3-isopropylmalate dehydrogenase (EC 1.1.1.85) | protein | 349 | 48% helix, 18% strand | Q5SIY4 |
| B | 3-isopropylmalate dehydrogenase (EC 1.1.1.85) | protein | 345 | 49% helix, 19% strand | Q5SIY4 |
Ligands and binding sites
- IPM · 3-isopropylmalic acid · ligand · 2 copies · chains A, B
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 2 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · chains A
- EOH · Ethanol · additive · 7 copies · 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
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 594 | 0.78 | 0.84 | 59 | MN, IPM, NAD |
| 2 | 607 | 0.77 | 0.83 | 62 | IPM, NAD, MN, GOL, EOH |
| 3 | 336 | 0.71 | 0.83 | 39 | EOH |
| 4 | 259 | 0.68 | 0.83 | 34 | EOH |
| 5 | 61 | 0.30 | 0.75 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 2641 Ų buried · 55 hydrogen bonds · protein-protein
Compared structures
- 4WUO · Structure of the E270A Mutant Isopropylmalate dehydrogenase from Thermus thermophilus in… · the same entry in another collection · chain A against A, TM-score 1.00
- Q5SIY4 · AlphaFold monomer V2.0 prediction for 3-isopropylmalate dehydrogenase (Q5SIY4) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 Q5SIY4
- Elsewhere: RCSB PDB 4WUO · PDBe 4WUO · UniProt Q5SIY4
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