Research workbench
Human IMPDH1 treated with ATP, imp, and NAD+, octamer-centered
Analyse Human IMPDH1 treated with ATP, imp, and NAD+, octamer-centered in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RES
- Type
- protein
- Length
- 3,856 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
- ATP, IMP, NAD
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 1 distinct chain · 33% 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 | 482 | 33% helix, 17% strand | P20839 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 16 copies · chains A, H, B, G, C, F, D, E
- 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 | 718 | 0.79 | 0.84 | 44 | empty |
| 2 | 769 | 0.79 | 0.83 | 61 | IMP, NAD |
| 3 | 720 | 0.79 | 0.83 | 44 | empty |
| 4 | 761 | 0.79 | 0.83 | 62 | IMP, NAD |
| 5 | 780 | 0.78 | 0.82 | 61 | IMP, NAD |
Interfaces
12 interfaces between chains.
- B–C · 2305 Ų buried · 36 hydrogen bonds · protein-protein
- F–G · 2300 Ų buried · 35 hydrogen bonds · protein-protein
- C–D · 2295 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 2294 Ų buried · 36 hydrogen bonds · protein-protein
- E–F · 2292 Ų buried · 34 hydrogen bonds · protein-protein
Compared structures
- 7RES · Human IMPDH1 treated with ATP, 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 0.87
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 7RES · PDBe 7RES · UniProt P20839
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