MolNFT v1 · #186483 · protein
Human retinal variant IMPDH1(595) treated with GTP, ATP, imp, NAD+, interface-centered
7RFI · Isoform 5 of inosine-5'-monophosphate dehydrogenase 1: “Human retinal variant IMPDH1(595) treated with GTP, ATP, imp, NAD+, interface-centered”. Electron microscopy, 3 ligands (GTP, IMP, NAD), 20 pockets (best druggability 0.85).…
- PDB
- 7RFI
- Type
- protein
- Length
- 3,376 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Isoform 5 of inosine-5'-monophosphate dehydrogenase 1
- EC
- 1.1.1.205
- Ligands
- GTP, IMP, NAD
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 1 distinct chain · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, G, H | Isoform 5 of inosine-5'-monophosphate dehydrogenase 1 (EC 1.1.1.205) | protein | 422 | 38% helix, 17% strand | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 16 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
- 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 480 | 0.85 | 0.92 | 75 | empty |
| 2 | 545 | 0.85 | 0.91 | 83 | empty |
| 3 | 688 | 0.85 | 0.89 | 90 | empty |
| 4 | 290 | 0.79 | 0.91 | 55 | empty |
| 5 | 1107 | 0.78 | 0.80 | 96 | IMP, NAD |
Interfaces
16 interfaces between chains.
- G–H · 2588 Ų buried · 34 hydrogen bonds · protein-protein
- E–H · 2584 Ų buried · 33 hydrogen bonds · protein-protein
- A–D · 2582 Ų buried · 33 hydrogen bonds · protein-protein
- F–G · 2578 Ų buried · 34 hydrogen bonds · protein-protein
- C–D · 2570 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 7RFI · Human retinal variant IMPDH1(595) treated with GTP, ATP, imp, NAD+, interface-centered · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 7RFI · PDBe 7RFI
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