Research workbench
Crystal structure of inosine monophosphate dehydrogenase in complex with mycophenolic acid
Analyse Crystal structure of inosine monophosphate dehydrogenase 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
- 1JR1
- Type
- protein
- Length
- 804 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inosine-5'-monophosphate dehydrogenase 2
- EC
- 1.1.1.205
- UniProt
- P12269
- Ligands
- IMP, MOA, K
- Pockets
- 9 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 35% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inosine-5'-monophosphate dehydrogenase 2 (EC 1.1.1.205) | protein | 436 | 34% helix, 19% strand | P12269 |
| B | Inosine-5'-monophosphate dehydrogenase 2 (EC 1.1.1.205) | protein | 368 | 37% helix, 19% strand | P12269 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 2 copies · chains A, B
- MOA · Mycophenolic acid · ligand · 2 copies · chains A, B
- K · Potassium ion · metal · 2 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.74 | 0.85 | 40 | IMP, MOA |
| 2 | 370 | 0.72 | 0.84 | 43 | IMP, MOA |
| 3 | 374 | 0.59 | 0.76 | 39 | empty |
| 4 | 127 | 0.38 | 0.74 | 19 | empty |
| 5 | 87 | 0.36 | 0.76 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 156 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 1JR1 · Crystal structure of Inosine Monophosphate Dehydrogenase in complex with Mycophenolic Acid · the same entry in another collection · chain A against A, TM-score 1.00
- P12269 · AlphaFold monomer V2.0 prediction for inosine-5'-monophosphate dehydrogenase 2 (P12269) · a predicted model of the same protein · chain B 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 P12269
- Elsewhere: RCSB PDB 1JR1 · PDBe 1JR1 · UniProt P12269
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.