Research workbench
Structure of human imp dehydrogenase, isoform 2, bound to GTP
Analyse Structure of human imp dehydrogenase, isoform 2, bound to GTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I0O
- Type
- protein
- Length
- 865 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
- P12268
- Ligands
- GTP, SO4
- Pockets
- 6 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Inosine-5'-monophosphate dehydrogenase 2 (EC 1.1.1.205) | protein | 434 | 38% helix, 19% strand | P12268 |
| B | Inosine-5'-monophosphate dehydrogenase 2 (EC 1.1.1.205) | protein | 431 | 38% helix, 18% strand | P12268 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 6 copies · chains A, B
- SO4 · Sulfate ion · ion · 26 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 614 | 0.69 | 0.77 | 60 | GTP |
| 2 | 166 | 0.52 | 0.78 | 22 | GTP |
| 3 | 74 | 0.43 | 0.81 | 20 | empty |
| 4 | 87 | 0.42 | 0.79 | 21 | empty |
| 5 | 62 | 0.31 | 0.75 | 15 | SO4 |
Interfaces
1 interface between chains.
- A–B · 942 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6I0O · Structure of human IMP dehydrogenase, isoform 2, bound to GTP · the same entry in another collection · chain A against A, TM-score 1.00
- P12268 · AlphaFold monomer V2.0 prediction for inosine-5'-monophosphate dehydrogenase 2 (P12268) · 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 P12268
- Elsewhere: RCSB PDB 6I0O · PDBe 6I0O · UniProt P12268
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