MolNFT v1 · #166026 · protein
Human IMPDH2 treated with ATP, imp, and 20 mm GTP. filament assembly interface reconstruction.
6UDP · Inosine-5'-monophosphate dehydrogenase 2: “Human IMPDH2 treated with ATP, imp, and 20 mm GTP. filament assembly interface reconstruction.”. Electron microscopy, 1 ligand (IMP), 20 pockets (best druggability 0.80). MolNFT v1 #166026…
- PDB
- 6UDP
- Type
- protein
- Length
- 3,008 residues
- Chains
- 8
- 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
- IMP
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 1 distinct chain · 32% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Inosine-5'-monophosphate dehydrogenase 2 (EC 1.1.1.205) | protein | 376 | 32% helix, 20% strand | P12268 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, 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 | 586 | 0.80 | 0.86 | 104 | empty |
| 2 | 663 | 0.77 | 0.83 | 53 | IMP |
| 3 | 696 | 0.77 | 0.82 | 56 | IMP |
| 4 | 654 | 0.77 | 0.82 | 53 | IMP |
| 5 | 683 | 0.77 | 0.82 | 58 | IMP |
Interfaces
16 interfaces between chains.
- G–H · 2359 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2359 Ų buried · 32 hydrogen bonds · protein-protein
- F–G · 2354 Ų buried · 32 hydrogen bonds · protein-protein
- A–D · 2351 Ų buried · 32 hydrogen bonds · protein-protein
- B–C · 2350 Ų buried · 32 hydrogen bonds · protein-protein
Compared structures
- 6UDP · Human IMPDH2 treated with ATP, IMP, and 20 mM GTP. Filament assembly interface… · the same entry in another collection · chain H against H, 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 0.96
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 6UDP · PDBe 6UDP · UniProt P12268
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