MolNFT v1 · #165864 · protein
Human IMPDH2 treated with ATP, imp, and NAD+. bent (1/4 compressed, 3/4 extended) segment reconstruction.
6U8R · Inosine-5'-monophosphate dehydrogenase 2: “Human IMPDH2 treated with ATP, imp, and NAD+. bent (1/4 compressed, 3/4 extended) segment reconstruction.”. Electron microscopy, 3 ligands (ATP, IMP, NAD), 20 pockets (best druggability…
- PDB
- 6U8R
- 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 0.79
Structure
electron microscopy · 2 distinct chains · 29% helix, 17% 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 | 29% helix, 17% strand | P12268 |
| M, N, O, P, I, J, K, L | Inosine-5'-monophosphate dehydrogenase 2 (EC 1.1.1.205) | protein | 14 | 29% helix, 0% strand | P12268 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 16 copies · chains A, H, B, G, C, F, D, E
- 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 | 805 | 0.79 | 0.83 | 66 | IMP, NAD |
| 2 | 608 | 0.78 | 0.84 | 58 | IMP, NAD |
| 3 | 682 | 0.78 | 0.83 | 61 | IMP, NAD |
| 4 | 801 | 0.78 | 0.81 | 63 | IMP, NAD |
| 5 | 714 | 0.78 | 0.82 | 60 | IMP, NAD |
Interfaces
20 interfaces between chains.
- E–F · 2418 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 2352 Ų buried · 33 hydrogen bonds · protein-protein
- F–G · 2335 Ų buried · 26 hydrogen bonds · protein-protein
- E–H · 2328 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 2320 Ų buried · 27 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6U8R · Human IMPDH2 treated with ATP, IMP, and NAD+. Bent (1/4 compressed, 3/4 extended) segment… · the same entry in another collection · chain L against L, 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 6U8R · PDBe 6U8R · UniProt P12268
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