Research workbench
Complex of mitochondrial isocitrate dehydrogenase R140Q mutant with agi-6780 inhibitor
Analyse Complex of mitochondrial isocitrate dehydrogenase R140Q mutant with agi-6780… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JA8
- Type
- protein
- Length
- 822 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NADP], mitochondrial
- EC
- 1.1.1.42
- UniProt
- P48735
- Ligands
- NDP, 1K9, CA
- Pockets
- 9 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP], mitochondrial (EC 1.1.1.42) | protein | 416 | 48% helix, 21% strand | P48735 |
| B | Isocitrate dehydrogenase [NADP], mitochondrial (EC 1.1.1.42) | protein | 406 | 48% helix, 22% strand | P48735 |
Ligands and binding sites
- NDP · Nadph dihydro-nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- 1K9 · 1-[5-(cyclopropylsulfamoyl)-2-thiophen-3-yl-phenyl]-3-[3-(trifluoromethyl)phenyl]urea · ligand · chains A, B
- CA · Calcium ion · metal · 2 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
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 168 | 0.83 | 0.97 | 33 | 1K9 |
| 2 | 821 | 0.68 | 0.75 | 69 | NDP |
| 3 | 296 | 0.62 | 0.80 | 30 | empty |
| 4 | 289 | 0.59 | 0.78 | 31 | empty |
| 5 | 281 | 0.53 | 0.76 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 3048 Ų buried · 47 hydrogen bonds · protein-protein
Compared structures
- 4JA8 · Complex of Mitochondrial Isocitrate Dehydrogenase R140Q Mutant with AGI-6780 Inhibitor · the same entry in another collection · chain A against A, TM-score 1.00
- P48735 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP], mitochondrial… · 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 P48735
- Elsewhere: RCSB PDB 4JA8 · PDBe 4JA8 · UniProt P48735
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