Research workbench
RAS:SOS:RAS in complex with a small molecule activator
Analyse RAS:SOS:RAS in complex with a small molecule activator in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BVM
- 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, EBV, MG, NA
- Pockets
- 9 · 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
- EBV · (2S)-2-amino-1-[(3ar,6as)-5-[(5-chloro-1H-indol-3-yl) methyl]hexahydropyrrolo[3,4-c]pyrrol-2(1H)-yl]-3-(1H-indol-3-yl)propan-1-one · 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
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1167 | 0.78 | 0.80 | 105 | GNP, MG |
| 2 | 317 | 0.71 | 0.84 | 49 | empty |
| 3 | 305 | 0.63 | 0.80 | 48 | empty |
| 4 | 208 | 0.51 | 0.76 | 32 | GOL |
| 5 | 176 | 0.50 | 0.77 | 40 | FMT |
Interfaces
2 interfaces between chains.
- B–C · 1797 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 1562 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 6BVM · PDBe 6BVM · UniProt P01112 · UniProt Q07889
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