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
- 7RGQ
- Type
- protein
- Length
- 3,848 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
- GTP, NAD, IMP, ATP
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 1 distinct chain · 31% helix, 20% 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 | 481 | 31% helix, 20% strand | P20839 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 16 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
- IMP · Inosinic acid · ligand · 8 copies · chains A, B, C, D, E, F, G, H
- ATP · Adenosine-5'-triphosphate · ligand · 8 copies · chains A, H, B, G, C, F, D, E
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 | 1002 | 0.84 | 0.85 | 94 | NAD, IMP |
| 2 | 1000 | 0.84 | 0.85 | 94 | NAD, IMP |
| 3 | 1020 | 0.84 | 0.85 | 94 | NAD, IMP |
| 4 | 1084 | 0.83 | 0.84 | 96 | NAD, IMP |
| 5 | 1091 | 0.83 | 0.84 | 96 | NAD, IMP |
Interfaces
20 interfaces between chains.
- E–H · 2380 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 2374 Ų buried · 29 hydrogen bonds · protein-protein
- E–F · 2363 Ų buried · 32 hydrogen bonds · protein-protein
- F–G · 2361 Ų buried · 30 hydrogen bonds · protein-protein
- A–D · 2355 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 7RGQ · 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 7RGQ · PDBe 7RGQ · UniProt P20839
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