Research workbench

Ligand-bound RAS:SOS:RAS complex

Analyse Ligand-bound RAS:SOS:RAS complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WFP
Type: protein
Length: 801 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, 5UX, MG
Pockets: 8 · best druggability 0.78

Structure

x-ray diffraction · 3 distinct chains · 49% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
Q	GTPase HRAS	protein	166	39% helix, 27% strand	P01112
R	GTPase HRAS	protein	167	34% helix, 26% strand	P01112
N	Son of sevenless homolog 1	protein	468	58% helix, 4% strand	Q07889

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains Q
5UX · 6-chloranyl-~{N}-(3-chloranyl-4-fluoranyl-phenyl)-1,2, 3,4-tetrahydroacridin-9-amine · ligand · chains N
MG · Magnesium ion · metal · chains Q

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	792	0.78	0.81	80	MG, GNP
2	259	0.71	0.86	41	empty
3	239	0.58	0.79	41	empty
4	132	0.57	0.82	19	5UX
5	274	0.55	0.77	53	empty

Interfaces

2 interfaces between chains.

R–N · 1809 Å² buried · 28 hydrogen bonds · protein-protein
Q–N · 1610 Å² buried · 30 hydrogen bonds · protein-protein

Compared structures

5WFP · Ligand-bound Ras:SOS:Ras complex · 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 N 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 5WFP · PDBe 5WFP · UniProt P01112 · UniProt Q07889

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