MolNFT v1 · #176953 · protein
Crystal structure of isocitrate dehydrogenase from ostreococcus tauri in complex with isocitrate and MAGNESIUM(II)
7E2W · Isocitrate dehydrogenase (NAD(+)), mitochondrial: “Crystal structure of isocitrate dehydrogenase from ostreococcus tauri in complex with isocitrate and…”. X-ray diffraction, 2 ligands (ICT, MG), 16 pockets (best druggability 0.69).…
- PDB
- 7E2W
- Type
- protein
- Length
- 1,603 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase (NAD(+)), mitochondrial
- EC
- 1.1.1.41
- UniProt
- A0A096P8D3
- Ligands
- ICT, MG
- Pockets
- 16 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase (NAD(+)), mitochondrial (EC 1.1.1.41) | protein | 403 | 45% helix, 23% strand | A0A096P8D3 |
| B | Isocitrate dehydrogenase (NAD(+)), mitochondrial (EC 1.1.1.41) | protein | 404 | 44% helix, 23% strand | A0A096P8D3 |
| C | Isocitrate dehydrogenase (NAD(+)), mitochondrial (EC 1.1.1.41) | protein | 400 | 42% helix, 23% strand | A0A096P8D3 |
| D | Isocitrate dehydrogenase (NAD(+)), mitochondrial (EC 1.1.1.41) | protein | 396 | 43% helix, 24% strand | A0A096P8D3 |
Ligands and binding sites
- ICT · Isocitric acid · ligand · chains A, B
- MG · Magnesium ion · metal · chains A, B
- IPA · Isopropyl alcohol · additive · 3 copies · chains A, C, D
- GOL · Glycerol · additive · 3 copies · chains C, D
- FLC · Citrate anion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.69 | 0.98 | 16 | empty |
| 2 | 606 | 0.69 | 0.78 | 51 | ICT, MG |
| 3 | 529 | 0.65 | 0.77 | 53 | GOL |
| 4 | 506 | 0.64 | 0.77 | 45 | empty |
| 5 | 474 | 0.60 | 0.75 | 51 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3201 Ų buried · 73 hydrogen bonds · protein-protein
- C–D · 3191 Ų buried · 68 hydrogen bonds · protein-protein
- A–D · 314 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 80 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7E2W · Crystal structure of isocitrate dehydrogenase from Ostreococcus tauri in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
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 A0A096P8D3
- Elsewhere: RCSB PDB 7E2W · PDBe 7E2W · UniProt A0A096P8D3
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