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: 6D5V
Type: protein
Length: 800 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, FVY, MG
Pockets: 11 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 50% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
Q	GTPase HRAS	protein	166	40% helix, 27% strand	P01112
R	GTPase HRAS	protein	167	35% helix, 26% strand	P01112
S	Son of sevenless homolog 1	protein	467	58% helix, 4% strand	Q07889

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains Q
FVY · 1-[(3-chloro-4-fluorophenyl)methyl]-5,6-dimethyl-1H-benzimidazol-2-amine · 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, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1027	0.78	0.80	102	MG, GNP
2	289	0.69	0.84	43	empty
3	52	0.65	0.95	18	empty
4	275	0.61	0.79	41	empty
5	150	0.60	0.83	21	FVY

Interfaces

2 interfaces between chains.

R–S · 1729 Å² buried · 24 hydrogen bonds · protein-protein
Q–S · 1530 Å² buried · 23 hydrogen bonds · protein-protein

Compared structures

6D5V · Ras:SOS:Ras in complex with a small molecule activator · the same entry in another collection · chain Q against Q, TM-score 1.00
Q07889 · AlphaFold monomer V2.0 prediction for son of sevenless homolog 1 (Q07889) · a predicted model of the same protein · chain S against A, TM-score 0.93

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 6D5V · PDBe 6D5V · UniProt P01112 · UniProt Q07889

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