Research workbench
KRAS-169 Q61H gppnhp + ch-3
Analyse KRAS-169 Q61H gppnhp + ch-3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6GQY
- Type
- protein
- Length
- 1,001 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.75
- Source
- Homo sapiens
- Molecule
- GTPase KRas
- UniProt
- P01116
- Ligands
- GNP, F8Q, MG
- Pockets
- 16 · best druggability 0.80
Structure
x-ray diffraction · resolution 2.75 · 4 distinct chains · 36% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | GTPase KRas | protein | 171 | 36% helix, 25% strand | P01116 |
| C | GTPase KRas | protein | 165 | 35% helix, 25% strand | P01116 |
| D, E | GTPase KRas | protein | 164 | 35% helix, 26% strand | P01116 |
| F | GTPase KRas | protein | 166 | 37% helix, 25% strand | P01116 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 6 copies · chains A, B, C, D, E, F
- F8Q · [4-[[3-fluoranyl-2-methoxy-4-(3-methoxyphenyl) phenyl]amino]phenyl]methyl-dimethyl-azanium · ligand · 4 copies · chains A, C, B, E, D, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 605 | 0.80 | 0.85 | 88 | empty |
| 2 | 547 | 0.78 | 0.85 | 91 | empty |
| 3 | 231 | 0.64 | 0.82 | 36 | MG, GNP |
| 4 | 181 | 0.62 | 0.83 | 36 | MG, GNP |
| 5 | 243 | 0.60 | 0.80 | 34 | MG, GNP |
Interfaces
12 interfaces between chains.
- B–E · 766 Ų buried · 12 hydrogen bonds · protein-protein
- D–F · 713 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 677 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 369 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 364 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6GQY · KRAS-169 Q61H gppnhp + ch-3 · 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
- Every structure of UniProt P01116
- Elsewhere: RCSB PDB 6GQY · PDBe 6GQY · UniProt P01116
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