MolNFT v1 · #166025 · protein
Human IMPDH2 treated with ATP, imp, and 20 mm GTP. fully compressed filament segment reconstruction.
6UDO · Inosine-5'-monophosphate dehydrogenase 2: “Human IMPDH2 treated with ATP, imp, and 20 mm GTP. fully compressed filament segment reconstruction.”. Electron microscopy, 3 ligands (GTP, IMP, ATP), 20 pockets (best druggability 0.75).…
- PDB
- 6UDO
- Type
- protein
- Length
- 4,008 residues
- Chains
- 16
- 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 0.75
Structure
electron microscopy · 2 distinct chains · 30% 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 | 487 | 30% helix, 20% strand | P12268 |
| I, J, K, L, M, N, O, P | Inosine-5'-monophosphate dehydrogenase 2 (EC 1.1.1.205) | protein | 14 | 29% helix, 0% strand | P12268 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 16 copies · chains A, B, C, D, E, F, G, H
- IMP · Inosinic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ATP · Adenosine-5'-triphosphate · ligand · 8 copies · chains A, F, B, E, C, H, D, 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 | 690 | 0.75 | 0.81 | 57 | IMP |
| 2 | 620 | 0.75 | 0.82 | 56 | IMP |
| 3 | 635 | 0.75 | 0.81 | 59 | IMP |
| 4 | 635 | 0.75 | 0.81 | 62 | IMP |
| 5 | 627 | 0.74 | 0.81 | 57 | IMP |
Interfaces
20 interfaces between chains.
- B–C · 2420 Ų buried · 38 hydrogen bonds · protein-protein
- E–H · 2420 Ų buried · 38 hydrogen bonds · protein-protein
- C–D · 2419 Ų buried · 38 hydrogen bonds · protein-protein
- A–D · 2418 Ų buried · 38 hydrogen bonds · protein-protein
- F–G · 2417 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 6UDO · Human IMPDH2 treated with ATP, IMP, and 20 mM GTP. Fully compressed filament segment… · the same entry in another collection · chain P against P, 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 6UDO · PDBe 6UDO · UniProt P12268
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