Research workbench
Crystal structure of the high affinity KRas mutant PDE6D complex
Analyse Crystal structure of the high affinity KRas mutant PDE6D complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Q9U
- Type
- protein
- Length
- 641 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.238
- Source
- Homo sapiens
- Molecule
- GTPase KRas; Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit…
- EC
- 3.6.5.2
- UniProt
- P01116, O43924
- Ligands
- GDP, FAR, SO4
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.238 · 4 distinct chains · 29% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| AAA | GTPase KRas (EC 3.6.5.2) | protein | 170 | 40% helix, 25% strand | P01116 |
| BBB | GTPase KRas (EC 3.6.5.2) | protein | 174 | 41% helix, 24% strand | P01116 |
| DDD | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | protein | 147 | 15% helix, 60% strand | O43924 |
| CCC | Retinal rod rhodopsin-sensitive cGMP 3',5'-cyclic phosphodiesterase subunit delta | protein | 150 | 16% helix, 59% strand | O43924 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains AAA, BBB
- FAR · Farnesyl · ligand · 2 copies · chains AAA, DDD, BBB, CCC
- SO4 · Sulfate ion · ion · 3 copies · chains BBB, AAA, DDD, CCC
- EDO · 1,2-ethanediol · additive · 5 copies · chains DDD, CCC
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 173 | 0.83 | 0.97 | 29 | FAR, SO4 |
| 2 | 174 | 0.83 | 0.97 | 29 | FAR, SO4 |
| 3 | 105 | 0.32 | 0.72 | 19 | empty |
| 4 | 52 | 0.32 | 0.77 | 13 | empty |
Interfaces
3 interfaces between chains.
- AAA–DDD · 633 Ų buried · 8 hydrogen bonds · protein-protein
- BBB–CCC · 612 Ų buried · 9 hydrogen bonds · protein-protein
- AAA–BBB · 70 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 lipid, 2 modified (farnesylation, nonstandard).
Compared structures
- O43924 · AlphaFold monomer V2.0 prediction for retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic… · a predicted model of the same protein · chain DDD against A, TM-score 0.98
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 P01116
- Every structure of UniProt O43924
- Elsewhere: RCSB PDB 7Q9U · PDBe 7Q9U · UniProt P01116 · UniProt O43924
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