Research workbench
Structure of the E270A mutant isopropylmalate dehydrogenase from thermus thermophilus in complex with ipm, mn and NADH
Analyse Structure of the E270A mutant isopropylmalate dehydrogenase from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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