Research workbench
Human IMPDH2 treated with ATP, imp, NAD+, and 2 mm GTP. filament assembly interface reconstruction.
Analyse Human IMPDH2 treated with ATP, imp, NAD+, and 2 mm GTP. filament assembly… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U8S
- 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, NAD
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 34% helix, 18% 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 | 34% helix, 18% strand | P12268 |
Ligands and binding sites
- IMP · Inosinic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, D, B, C, E, H, F, G
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 | 979 | 0.85 | 0.86 | 156 | empty |
| 2 | 710 | 0.78 | 0.83 | 61 | IMP, NAD |
| 3 | 742 | 0.78 | 0.82 | 58 | IMP, NAD |
| 4 | 744 | 0.78 | 0.82 | 62 | IMP, NAD |
| 5 | 741 | 0.78 | 0.82 | 62 | IMP, NAD |
Interfaces
16 interfaces between chains.
- E–F · 2273 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2272 Ų buried · 34 hydrogen bonds · protein-protein
- E–H · 2268 Ų buried · 33 hydrogen bonds · protein-protein
- G–H · 2268 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 2268 Ų buried · 35 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 6U8S · Human IMPDH2 treated with ATP, IMP, NAD+, and 2 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 6U8S · PDBe 6U8S · UniProt P12268
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