Research workbench
3D structure of E. COLI isocitrate dehydrogenase K100M mutant in complex with alpha-ketoglutarate, MAGNESIUM(II) and NADPH - the product complex
Analyse 3D structure of E. COLI isocitrate dehydrogenase K100M mutant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4AJR
- Type
- protein
- Length
- 415 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NADP]
- EC
- 1.1.1.42
- UniProt
- P08200
- Ligands
- NMN, NAP, AKG, MG
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 415 | 42% helix, 18% strand | P08200 |
Ligands and binding sites
- NMN · Beta-nicotinamide ribose monophosphate · ligand · chains A
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- AKG · 2-oxoglutaric acid · ligand · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 353 | 0.59 | 0.76 | 37 | empty |
| 2 | 215 | 0.48 | 0.75 | 36 | AKG, MG |
| 3 | 61 | 0.37 | 0.78 | 14 | empty |
Compared structures
- 4AJR · 3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- P08200 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP] (P08200) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P08200
- Elsewhere: RCSB PDB 4AJR · PDBe 4AJR · UniProt P08200
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