Research workbench
Human IMPDH2 treated with ATP, imp, and NAD+. fully extended filament segment reconstruction.
Analyse Human IMPDH2 treated with ATP, imp, and NAD+. fully extended filament segment… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6U8N
- 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
- ATP, IMP, NAD
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 2 distinct chains · 30% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 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 |
| A, B, C, D, E, F, G, H | Inosine-5'-monophosphate dehydrogenase 2 (EC 1.1.1.205) | protein | 488 | 31% helix, 18% strand | P12268 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 16 copies · chains A, G, B, F, C, E, D, H
- IMP · Inosinic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- NAD · Nicotinamide-adenine-dinucleotide · 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 | 653 | 0.78 | 0.83 | 58 | IMP, NAD |
| 2 | 667 | 0.78 | 0.83 | 59 | IMP, NAD |
| 3 | 668 | 0.78 | 0.83 | 59 | IMP, NAD |
| 4 | 701 | 0.78 | 0.83 | 58 | IMP, NAD |
| 5 | 690 | 0.78 | 0.83 | 60 | IMP, NAD |
Interfaces
20 interfaces between chains.
- E–F · 2288 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2285 Ų buried · 34 hydrogen bonds · protein-protein
- E–H · 2285 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 2283 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2280 Ų buried · 34 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 covalent (covalent ligand).
Compared structures
- 6U8N · Human IMPDH2 treated with ATP, IMP, and NAD+. Fully extended filament segment… · the same entry in another collection · chain H against H, 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 6U8N · PDBe 6U8N · UniProt P12268
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