Research workbench
Crystal structure of saccharomyces cerevesiae mitochondrial NADP(+)- dependent isocitrate dehydrogenase in complex with NADP(+)
Analyse Crystal structure of saccharomyces cerevesiae mitochondrial NADP(+)- dependent… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QFV
- Type
- protein
- Length
- 1,636 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NADP]
- EC
- 1.1.1.42
- UniProt
- P21954
- Ligands
- NAP
- Pockets
- 19 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 47% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 410 | 46% helix, 23% strand | P21954 |
| B | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 408 | 47% helix, 22% strand | P21954 |
| C | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 408 | 47% helix, 22% strand | P21954 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1030 | 0.84 | 0.85 | 103 | NAP |
| 2 | 792 | 0.68 | 0.75 | 62 | NAP |
| 3 | 620 | 0.67 | 0.77 | 66 | NAP |
| 4 | 136 | 0.66 | 0.88 | 26 | empty |
| 5 | 215 | 0.62 | 0.83 | 31 | empty |
Interfaces
5 interfaces between chains.
- C–D · 3284 Ų buried · 54 hydrogen bonds · protein-protein
- A–B · 3278 Ų buried · 52 hydrogen bonds · protein-protein
- A–D · 536 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 484 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 145 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2QFV · Crystal structure of Saccharomyces cerevesiae mitochondrial NADP(+)-dependent isocitrate… · the same entry in another collection · chain A against A, TM-score 1.00
- P21954 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP], mitochondrial… · a predicted model of the same protein · chain B against A, TM-score 0.94
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 P21954
- Elsewhere: RCSB PDB 2QFV · PDBe 2QFV · UniProt P21954
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