MolNFT v1 · #165895 · protein
Human IMPDH2 treated with ATP, imp, NAD+, and 2 mm GTP. fully compressed filament segment reconstruction.
6U9O · Inosine-5'-monophosphate dehydrogenase 2: “Human IMPDH2 treated with ATP, imp, NAD+, and 2 mm GTP. fully compressed filament segment reconstruction.”. Electron microscopy, 4 ligands (GTP, ATP, IMP), 20 pockets (best druggability…
- PDB
- 6U9O
- Type
- protein
- Length
- 4,016 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, ATP, IMP, NAD
- Pockets
- 20 · best druggability 0.77
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 | 488 | 31% helix, 20% strand | P12268 |
| I, J, K, L, M, N, O, P | Inosine-5'-monophosphate dehydrogenase 2 (EC 1.1.1.205) | protein | 14 | 0% helix, 0% strand | P12268 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 16 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
- 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 | 684 | 0.77 | 0.83 | 62 | IMP, NAD |
| 2 | 689 | 0.77 | 0.82 | 62 | IMP, NAD |
| 3 | 697 | 0.77 | 0.82 | 64 | IMP, NAD |
| 4 | 695 | 0.77 | 0.82 | 62 | IMP, NAD |
| 5 | 708 | 0.77 | 0.82 | 62 | IMP, NAD |
Interfaces
28 interfaces between chains.
- B–C · 2433 Ų buried · 40 hydrogen bonds · protein-protein
- E–H · 2426 Ų buried · 39 hydrogen bonds · protein-protein
- C–D · 2426 Ų buried · 36 hydrogen bonds · protein-protein
- A–D · 2424 Ų buried · 39 hydrogen bonds · protein-protein
- F–G · 2422 Ų buried · 39 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 6U9O · Human IMPDH2 treated with ATP, IMP, NAD+, and 2 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 6U9O · PDBe 6U9O · UniProt P12268
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