Research workbench
Crystal structure of isocitrate dehydrogenase from ostreococcus tauri in complex with isocitrate and MAGNESIUM(II)
Analyse Crystal structure of isocitrate dehydrogenase from ostreococcus tauri in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.