Research workbench
Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in complex with NADP, isocitrate, and CALCIUM(2+)
Analyse Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1T0L
- Type
- protein
- Length
- 1,656 residues
- Chains
- 4
- 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
- NAP, ICT, CA
- Pockets
- 18 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 47% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 414 | 47% helix, 22% strand | O75874 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
- ICT · Isocitric acid · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1052 | 0.80 | 0.81 | 84 | NAP, ICT |
| 2 | 1152 | 0.79 | 0.81 | 96 | CA, NAP, ICT |
| 3 | 1114 | 0.79 | 0.81 | 93 | CA, NAP, ICT |
| 4 | 982 | 0.79 | 0.81 | 82 | NAP, ICT |
| 5 | 80 | 0.76 | 0.98 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 3954 Ų buried · 66 hydrogen bonds · protein-protein
- C–D · 3862 Ų buried · 69 hydrogen bonds · protein-protein
- B–C · 490 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1T0L · Crystal structure of human cytosolic NADP(+)-dependent isocitrate dehydrogenase in… · the same entry in another collection · chain A against A, TM-score 1.00
- O75874 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP] cytoplasmic (O75874) · a predicted model of the same protein · chain A 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 O75874
- Elsewhere: RCSB PDB 1T0L · PDBe 1T0L · UniProt O75874
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