Research workbench
Crystal structure of mouse cytosolic isocitrate dehydrogenase complexed with cadmium
Analyse Crystal structure of mouse cytosolic isocitrate dehydrogenase complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YZI
- Type
- protein
- Length
- 817 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NADP] cytoplasmic
- EC
- 1.1.1.42
- UniProt
- O88844
- Ligands
- NAP, CD
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 409 | 48% helix, 23% strand | O88844 |
| B | Isocitrate dehydrogenase [NADP] cytoplasmic (EC 1.1.1.42) | protein | 408 | 48% helix, 23% strand | O88844 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · 2 copies · chains A, B
- CD · Cadmium ion · metal · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 906 | 0.79 | 0.81 | 74 | NAP |
| 2 | 726 | 0.76 | 0.81 | 63 | CD, NAP |
| 3 | 178 | 0.48 | 0.77 | 25 | empty |
| 4 | 115 | 0.48 | 0.80 | 20 | empty |
| 5 | 154 | 0.45 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 3855 Ų buried · 63 hydrogen bonds · protein-protein
Compared structures
- 5YZI · Crystal Structure of Mouse Cytosolic Isocitrate Dehydrogenase complexed with Cadmium · the same entry in another collection · chain A against A, TM-score 1.00
- O88844 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP] cytoplasmic (O88844) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 O88844
- Elsewhere: RCSB PDB 5YZI · PDBe 5YZI · UniProt O88844
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