Research workbench
Human IMPDH2 treated with ATP, imp, and 20 mm GTP. filament assembly interface reconstruction.
Analyse Human IMPDH2 treated with ATP, imp, and 20 mm GTP. filament assembly interface… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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