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