MolNFT v1 · #87003 · protein
3D structure of E. COLI isocitrate dehydrogenase K100M mutant in complex with isocitrate and MAGNESIUM(II)
4BNP · Isocitrate dehydrogenase [NADP]: “3D structure of E. COLI isocitrate dehydrogenase K100M mutant in complex with isocitrate and MAGNESIUM(II)”. X-ray diffraction, 3 ligands (ICT, MG, SO4), 3 pockets (best druggability 0.63). MolNFT…
- 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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