Research workbench
Human retinal variant IMPDH1(595) treated with ATP, octamer-centered
Analyse Human retinal variant IMPDH1(595) treated with ATP, octamer-centered in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7RFH
- Type
- protein
- Length
- 3,595 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
- ATP
- Pockets
- 20 · best druggability 0.77
Structure
electron microscopy · 3 distinct chains · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Isoform 5 of inosine-5'-monophosphate dehydrogenase 1 (EC 1.1.1.205) | protein | 449 | 36% helix, 15% strand | — |
| G | Isoform 5 of inosine-5'-monophosphate dehydrogenase 1 (EC 1.1.1.205) | protein | 450 | 35% helix, 16% strand | — |
| H | Isoform 5 of inosine-5'-monophosphate dehydrogenase 1 (EC 1.1.1.205) | protein | 451 | 35% helix, 16% strand | — |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 16 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 | 831 | 0.77 | 0.81 | 77 | empty |
| 2 | 732 | 0.77 | 0.82 | 58 | empty |
| 3 | 664 | 0.71 | 0.78 | 65 | ATP |
| 4 | 259 | 0.69 | 0.85 | 41 | empty |
| 5 | 610 | 0.69 | 0.78 | 51 | ATP |
Interfaces
12 interfaces between chains.
- B–C · 1567 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 1561 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 1558 Ų buried · 17 hydrogen bonds · protein-protein
- F–G · 1555 Ų buried · 16 hydrogen bonds · protein-protein
- E–H · 1551 Ų buried · 18 hydrogen bonds · protein-protein
Compared structures
- 7RFH · Human retinal variant IMPDH1(595) treated with ATP, octamer-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 7RFH · PDBe 7RFH
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