MolNFT v1 · #27214 · protein

Crystal structure of a ternary RAS:SOS:RAS*GDP complex

1XD2 · Transforming protein P21/H-RAS-1: “Crystal structure of a ternary RAS:SOS:RAS*GDP complex”. X-ray diffraction, 3 ligands (GDP, MG, PO4), 10 pockets (best druggability 0.84). MolNFT v1 #27214 on GenesisL1: 3D structure, binding sites…

PDB: 1XD2
Type: protein
Length: 801 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transforming protein P21/H-RAS-1; Son of sevenless protein homolog 1
UniProt: P01112, Q07889
Ligands: GDP, MG, PO4
Pockets: 10 · best druggability 0.84

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transforming protein P21/H-RAS-1	protein	166	39% helix, 27% strand	P01112
B	Transforming protein P21/H-RAS-1	protein	166	37% helix, 24% strand	P01112
C	Son of sevenless protein homolog 1	protein	469	58% helix, 3% strand	Q07889

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · chains A
MG · Magnesium ion · metal · chains A
PO4 · Phosphate ion · ion · 4 copies · chains A, B, C

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

Pockets

10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1087	0.84	0.85	132	MG, PO4, GDP
2	344	0.63	0.79	45	empty
3	244	0.52	0.76	49	PO4
4	212	0.51	0.76	33	empty
5	96	0.41	0.78	24	empty

Interfaces

2 interfaces between chains.

B–C · 1884 Å² buried · 28 hydrogen bonds · protein-protein
A–C · 1667 Å² buried · 27 hydrogen bonds · protein-protein

Compared structures

1XD2 · Crystal Structure of a ternary Ras:SOS:Ras*GDP complex · the same entry in another collection · chain A against A, 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 C against A, TM-score 0.91

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 1XD2 · PDBe 1XD2 · UniProt P01112 · UniProt Q07889

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