MolNFT v1 · #166027 · protein
Human IMPDH2 treated with ATP, imp, and 20 mm GTP. fully compressed filament end reconstruction.
6UDQ · Inosine-5'-monophosphate dehydrogenase 2: “Human IMPDH2 treated with ATP, imp, and 20 mm GTP. fully compressed filament end reconstruction.”. Electron microscopy, 3 ligands (GTP, IMP, ATP), 20 pockets (best druggability 0.78).…
- PDB
- 6UDQ
- Type
- protein
- Length
- 3,956 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inosine-5'-monophosphate dehydrogenase 2
- EC
- 1.1.1.205
- UniProt
- P12268
- Ligands
- GTP, IMP, ATP
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 3 distinct chains · 32% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I, J, K, L | Inosine-5'-monophosphate dehydrogenase 2 (EC 1.1.1.205) | protein | 14 | 29% helix, 0% strand | P12268 |
| A, B, C, D | Inosine-5'-monophosphate dehydrogenase 2 (EC 1.1.1.205) | protein | 487 | 32% helix, 19% strand | P12268 |
| E, F, G, H | Inosine-5'-monophosphate dehydrogenase 2 (EC 1.1.1.205) | protein | 488 | 32% helix, 19% strand | P12268 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 16 copies · chains A, E, B, F, C, G, D, H
- IMP · Inosinic acid · ligand · 8 copies · chains A, E, B, F, C, G, D, H
- ATP · Adenosine-5'-triphosphate · ligand · 8 copies · chains A, E, B, F, C, G, D, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.78 | 0.83 | 56 | IMP |
| 2 | 720 | 0.77 | 0.82 | 57 | IMP |
| 3 | 717 | 0.76 | 0.81 | 55 | IMP |
| 4 | 623 | 0.76 | 0.83 | 56 | IMP |
| 5 | 611 | 0.76 | 0.83 | 57 | IMP |
Interfaces
24 interfaces between chains.
- E–H · 2476 Ų buried · 31 hydrogen bonds · protein-protein
- G–H · 2420 Ų buried · 35 hydrogen bonds · protein-protein
- A–D · 2419 Ų buried · 39 hydrogen bonds · protein-protein
- E–F · 2418 Ų buried · 34 hydrogen bonds · protein-protein
- F–G · 2407 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 covalent (covalent ligand).
Compared structures
- 6UDQ · Human IMPDH2 treated with ATP, IMP, and 20 mM GTP. Fully compressed filament end… · the same entry in another collection · chain H against H, 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 P12268
- Elsewhere: RCSB PDB 6UDQ · PDBe 6UDQ · UniProt P12268
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