Research workbench
Crystal structure of monomeric isocitrate dehydrogenase from corynebacterium glutamicum in complex with NADP
Analyse Crystal structure of monomeric isocitrate dehydrogenase from corynebacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MBC
- Type
- protein
- Length
- 1,470 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isocitrate dehydrogenase [NADP]
- EC
- 1.1.1.42
- UniProt
- P50216
- Ligands
- NAP, MG
- Pockets
- 19 · best druggability 0.80
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Isocitrate dehydrogenase [NADP] (EC 1.1.1.42) | protein | 735 | 48% helix, 17% strand | P50216 |
Ligands and binding sites
- NAP · Nadp nicotinamide-adenine-dinucleotide phosphate · ligand · chains A
- 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
19 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 110 | 0.80 | 0.98 | 19 | empty |
| 2 | 101 | 0.80 | 0.99 | 20 | empty |
| 3 | 629 | 0.71 | 0.79 | 78 | empty |
| 4 | 660 | 0.70 | 0.78 | 60 | empty |
| 5 | 411 | 0.57 | 0.74 | 48 | empty |
Interfaces
1 interface between chains.
- A–B · 329 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 3MBC · Crystal structure of monomeric isocitrate dehydrogenase from Corynebacterium glutamicum… · the same entry in another collection · chain A against A, TM-score 1.00
- P50216 · AlphaFold monomer V2.0 prediction for isocitrate dehydrogenase [NADP] (P50216) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P50216
- Elsewhere: RCSB PDB 3MBC · PDBe 3MBC · UniProt P50216
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