MolNFT v1 · #186520 · protein
Human retinal variant IMPDH1(546) treated with ATP, imp, NAD+, interface-centered
7RGL · Inosine-5'-monophosphate dehydrogenase 1: “Human retinal variant IMPDH1(546) treated with ATP, imp, NAD+, interface-centered”. Electron microscopy, 2 ligands (IMP, NAD), 20 pockets (best druggability 0.82). MolNFT v1 #186520 on…
- PDB
- 7RGL
- Type
- protein
- Length
- 3,328 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Inosine-5'-monophosphate dehydrogenase 1
- EC
- 1.1.1.205
- UniProt
- P20839
- Ligands
- IMP, NAD
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 34% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Inosine-5'-monophosphate dehydrogenase 1 (EC 1.1.1.205) | protein | 416 | 34% helix, 19% strand | P20839 |
Ligands and binding sites
- 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 | 885 | 0.82 | 0.84 | 133 | empty |
| 2 | 733 | 0.78 | 0.82 | 60 | IMP, NAD |
| 3 | 981 | 0.78 | 0.80 | 87 | IMP, NAD |
| 4 | 1183 | 0.77 | 0.79 | 92 | empty |
| 5 | 983 | 0.77 | 0.80 | 92 | IMP, NAD |
Interfaces
16 interfaces between chains.
- E–F · 2327 Ų buried · 32 hydrogen bonds · protein-protein
- F–G · 2326 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2325 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 2323 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2322 Ų buried · 33 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 covalent (covalent ligand).
Compared structures
- 7RGL · Human retinal variant IMPDH1(546) treated with ATP, imp, NAD+, interface-centered · the same entry in another collection · chain H against H, TM-score 1.00
- P20839 · AlphaFold monomer V2.0 prediction for inosine-5'-monophosphate dehydrogenase 1 (P20839) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P20839
- Elsewhere: RCSB PDB 7RGL · PDBe 7RGL · UniProt P20839
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