MolNFT v1 · #146046 · protein
RAS:SOS:RAS in complex with a small molecule activator
6D5W · GTPase HRAS: “RAS:SOS:RAS in complex with a small molecule activator”. X-ray diffraction, 3 ligands (GNP, FVV, MG), 11 pockets (best druggability 0.80). MolNFT v1 #146046 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6D5W
- Type
- protein
- Length
- 803 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTPase HRAS; Son of sevenless homolog 1
- UniProt
- P01112, Q07889
- Ligands
- GNP, FVV, MG
- Pockets
- 11 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Q | GTPase HRAS | protein | 167 | 38% helix, 28% strand | P01112 |
| R | GTPase HRAS | protein | 167 | 34% helix, 26% strand | P01112 |
| S | Son of sevenless homolog 1 | protein | 469 | 59% helix, 4% strand | Q07889 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains Q
- FVV · 10-[(4-fluorophenyl)methyl]-2,3,4,10-tetrahydropyrimido[1,2-a]benzimidazole · ligand · chains S
- MG · Magnesium ion · metal · chains Q
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 981 | 0.80 | 0.81 | 101 | MG, GNP |
| 2 | 266 | 0.72 | 0.86 | 48 | empty |
| 3 | 51 | 0.66 | 0.96 | 15 | empty |
| 4 | 244 | 0.61 | 0.80 | 41 | empty |
| 5 | 148 | 0.60 | 0.83 | 23 | FVV |
Interfaces
2 interfaces between chains.
- R–S · 1765 Ų buried · 29 hydrogen bonds · protein-protein
- Q–S · 1599 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 6D5W · Ras:SOS:Ras in complex with a small molecule activator · the same entry in another collection · chain Q against Q, 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 P01112
- Every structure of UniProt Q07889
- Elsewhere: RCSB PDB 6D5W · PDBe 6D5W · UniProt P01112 · UniProt Q07889
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.