MolNFT v1 · #146024 · protein
RAS:SOS:RAS in complex with a small molecule activator
6D59 · GTPase HRAS: “RAS:SOS:RAS in complex with a small molecule activator”. X-ray diffraction, 4 ligands (GNP, FVJ, MG), 12 pockets (best druggability 0.78). MolNFT v1 #146024 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6D59
- Type
- protein
- Length
- 802 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, FVJ, MG, NA
- Pockets
- 12 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 49% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTPase HRAS | protein | 166 | 36% helix, 27% strand | P01112 |
| B | Son of sevenless homolog 1 | protein | 469 | 59% helix, 4% strand | Q07889 |
| C | GTPase HRAS | protein | 167 | 34% helix, 26% strand | P01112 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- FVJ · 6-chloro-4-(3,5-dimethyl-1H-pyrazol-4-yl)-1-[(4-fluoro-3,5-dimethylphenyl)methyl]-2-(piperazin-1-yl)-1H-benzimidazole · ligand · chains B
- MG · Magnesium ion · metal · chains A
- NA · Sodium ion · metal · chains C
- FMT · Formic acid · additive · 6 copies · chains B, A, C
- GOL · Glycerol · additive · 2 copies · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1081 | 0.78 | 0.80 | 97 | GNP, MG |
| 2 | 311 | 0.71 | 0.84 | 48 | empty |
| 3 | 57 | 0.67 | 0.96 | 17 | empty |
| 4 | 280 | 0.64 | 0.81 | 41 | empty |
| 5 | 146 | 0.58 | 0.82 | 18 | FVJ |
Interfaces
2 interfaces between chains.
- B–C · 1800 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1553 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
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 6D59 · PDBe 6D59 · UniProt P01112 · UniProt Q07889
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