Research workbench
Crystal structure analysis of human IDH1 mutants in complex with NADP+ and CA2+/ALPHA-ketoglutarate
Analyse Crystal structure analysis of human IDH1 mutants in complex with NADP+ and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4L04
- Type
- protein
- Length
- 2,471 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NADP] cytoplasmic
- EC
- 1.1.1.42
- UniProt
- O75874
- Ligands
- AKG, NAP, CA
- Pockets
- 20 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 48% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 411 | 48% helix, 22% strand | O75874 |
| B, D, F | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 412 | 47% helix, 23% strand | O75874 |
| C, E | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 412 | 47% helix, 23% strand | O75874 |
Ligands and binding sites
- AKG · 2-oxoglutaric acid · ligand · 6 copies · chains A, B, C, D, E, F
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 6 copies · chains A, B, C, D, E, F
- CA · Calcium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 943 | 0.79 | 0.81 | 73 | AKG, NAP |
| 2 | 980 | 0.78 | 0.80 | 82 | AKG, NAP |
| 3 | 945 | 0.78 | 0.80 | 81 | AKG, CA, NAP |
| 4 | 906 | 0.78 | 0.81 | 78 | AKG, NAP |
| 5 | 919 | 0.78 | 0.80 | 78 | AKG, CA, NAP |
Interfaces
7 interfaces between chains.
- E–F · 3765 Ų buried · 67 hydrogen bonds · protein-protein
- C–D · 3734 Ų buried · 68 hydrogen bonds · protein-protein
- A–B · 3707 Ų buried · 70 hydrogen bonds · protein-protein
- B–C · 322 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 289 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4L04 · Crystal Structure Analysis of human IDH1 mutants in complex with NADP+ and… · the same entry in another collection · chain F against F, TM-score 1.00
- O75874 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP] cytoplasmic (O75874) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 O75874
- Elsewhere: RCSB PDB 4L04 · PDBe 4L04 · UniProt O75874
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