MolNFT v1 · #186481 · protein
Human IMPDH1 treated with GTP, imp, and NAD+ octamer-centered
7RFG · Isoform 5 of inosine-5'-monophosphate dehydrogenase 1: “Human IMPDH1 treated with GTP, imp, and NAD+ octamer-centered”. Electron microscopy, 3 ligands (GTP, ATP, IMP), 20 pockets (best druggability 0.79). MolNFT v1 #186481 on…
- PDB
- 7RFG
- Type
- protein
- Length
- 3,928 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
- UniProt
- P20839
- Ligands
- GTP, ATP, IMP
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 1 distinct chain · 35% helix, 20% 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 | 491 | 35% helix, 20% strand | P20839 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 16 copies · chains A, B, C, D, E, F, G, H
- ATP · Adenosine-5'-triphosphate · ligand · 8 copies · chains A, G, B, F, C, E, D, H
- 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 800 | 0.79 | 0.83 | 63 | IMP |
| 2 | 787 | 0.79 | 0.83 | 63 | IMP |
| 3 | 821 | 0.78 | 0.82 | 62 | IMP |
| 4 | 767 | 0.78 | 0.83 | 63 | IMP |
| 5 | 698 | 0.78 | 0.83 | 61 | IMP |
Interfaces
20 interfaces between chains.
- B–C · 2431 Ų buried · 37 hydrogen bonds · protein-protein
- A–D · 2426 Ų buried · 41 hydrogen bonds · protein-protein
- F–G · 2409 Ų buried · 37 hydrogen bonds · protein-protein
- G–H · 2403 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 2401 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 7RFG · Human IMPDH1 treated with GTP, imp, and NAD+ octamer-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 7RFG · PDBe 7RFG · UniProt P20839
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