Research workbench
Human retinal variant IMPDH1(546) treated with GTP, ATP, imp, NAD+; interface-centered
Analyse Human retinal variant IMPDH1(546) treated with GTP, ATP, imp, NAD+… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RGI
- Type
- protein
- Length
- 2,856 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
- NAD, IMP
- Pockets
- 20 · best druggability 0.75
Structure
electron microscopy · 1 distinct chain · 36% helix, 16% 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 | 357 | 36% helix, 16% strand | P20839 |
Ligands and binding sites
- NAD · Nicotinamide-adenine-dinucleotide · ligand · 8 copies · chains A, D, B, C, E, H, F, G
- IMP · Inosinic acid · 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 453 | 0.75 | 0.84 | 72 | empty |
| 2 | 976 | 0.74 | 0.77 | 93 | NAD, IMP |
| 3 | 981 | 0.74 | 0.77 | 90 | NAD, IMP |
| 4 | 945 | 0.74 | 0.77 | 94 | NAD, IMP |
| 5 | 975 | 0.74 | 0.77 | 94 | NAD, IMP |
Interfaces
16 interfaces between chains.
- E–F · 2077 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 2065 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 2065 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 2064 Ų buried · 25 hydrogen bonds · protein-protein
- B–C · 2064 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 7RGI · Human retinal variant IMPDH1(546) treated with GTP, 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 0.99
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 7RGI · PDBe 7RGI · UniProt P20839
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