MolNFT v1 · #168819 · protein
Crystal structure of KRAS-G12D/K104Q mutant, GDP-bound
6WS4 · GTPase KRAS: “Crystal structure of KRAS-G12D/K104Q mutant, GDP-bound”. X-ray diffraction, 3 ligands (GDP, TCE, MG), 8 pockets (best druggability 0.63). MolNFT v1 #168819 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6WS4
- Type
- protein
- Length
- 676 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase KRAS
- UniProt
- P01116
- Ligands
- GDP, TCE, MG
- Pockets
- 8 · best druggability 0.63
Structure
x-ray diffraction · 1 distinct chain · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | GTPase KRAS | protein | 169 | 37% helix, 24% strand | P01116 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 4 copies · chains A, B, C, D
- TCE · 3,3',3''-phosphanetriyltripropanoic acid · ligand · chains B, C
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.63 | 0.79 | 49 | GDP, MG, TCE |
| 2 | 175 | 0.56 | 0.81 | 25 | empty |
| 3 | 161 | 0.52 | 0.79 | 36 | GDP, MG |
| 4 | 127 | 0.49 | 0.80 | 26 | GDP, MG |
| 5 | 136 | 0.47 | 0.78 | 30 | GDP, MG |
Interfaces
3 interfaces between chains.
- A–D · 297 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 291 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 13 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6WS4 · Crystal structure of KRAS-G12D/K104Q mutant, GDP-bound · 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 6WS4 · PDBe 6WS4 · UniProt P01116
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.