Research workbench
The crystal structure of isocitrate dehydrogenase KINASE/PHOSPHATASE from E. COLI
Analyse The crystal structure of isocitrate dehydrogenase KINASE/PHOSPHATASE from E.… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3EPS
- Type
- protein
- Length
- 1,125 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase KINASE/PHOSPHATASE
- EC
- 2.7.11.5, 3.1.3.-
- UniProt
- Q8X607
- Ligands
- AMP, ATP, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase KINASE/PHOSPHATASE (EC 2.7.11.5, 3.1.3.-) | protein | 566 | 44% helix, 17% strand | Q8X607 |
| B | Isocitrate dehydrogenase KINASE/PHOSPHATASE (EC 2.7.11.5, 3.1.3.-) | protein | 559 | 45% helix, 16% strand | Q8X607 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 2 copies · chains A, B
- ATP · Adenosine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.85 | 0.89 | 74 | AMP |
| 2 | 208 | 0.77 | 0.92 | 36 | empty |
| 3 | 219 | 0.76 | 0.91 | 35 | ATP, MG |
| 4 | 451 | 0.76 | 0.85 | 50 | AMP |
| 5 | 219 | 0.73 | 0.88 | 32 | ATP, MG |
Interfaces
1 interface between chains.
- A–B · 1033 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3EPS · The crystal structure of isocitrate dehydrogenase kinase/phosphatase from E. coli · the same entry in another collection · chain A against A, TM-score 1.00
- Q8X607 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase KINASE/PHOSPHATASE (Q8X607) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q8X607
- Elsewhere: RCSB PDB 3EPS · PDBe 3EPS · UniProt Q8X607
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