Research workbench
3D structure of E. COLI isocitrate dehydrogenase K100M mutant in complex with isocitrate and MAGNESIUM(II)
Analyse 3D structure of E. COLI isocitrate dehydrogenase K100M mutant in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BNP
- Type
- protein
- Length
- 415 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NADP]
- EC
- 1.1.1.42
- UniProt
- P08200
- Ligands
- ICT, MG, SO4
- Pockets
- 3 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 415 | 41% helix, 18% strand | P08200 |
Ligands and binding sites
- ICT · Isocitric acid · ligand · chains A
- MG · Magnesium ion · metal · chains A
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 433 | 0.63 | 0.77 | 47 | empty |
| 2 | 92 | 0.38 | 0.76 | 22 | empty |
| 3 | 70 | 0.30 | 0.74 | 17 | ICT, MG |
Compared structures
- 4BNP · 3D structure of E. coli Isocitrate Dehydrogenase K100M mutant in complex with isocitrate… · the same entry in another collection · chain A against A, TM-score 1.00
- P08200 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP] (P08200) · a predicted model of the same protein · 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 P08200
- Elsewhere: RCSB PDB 4BNP · PDBe 4BNP · UniProt P08200
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