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Choanoflagellate salpingoeca rosetta RAS with gmp-pnp

Analyse Choanoflagellate salpingoeca rosetta RAS with gmp-pnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5WDR
Type: protein
Length: 334 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS protein
EC: 3.6.5.2
UniProt: F2UBE5
Ligands: GNP, MG, NA
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	RAS protein (EC 3.6.5.2)	protein	167	39% helix, 28% strand	F2UBE5

Ligands and binding sites

GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	251	0.72	0.87	36	MG, GNP
2	440	0.63	0.77	64	MG, GNP

Interfaces

1 interface between chains.

A–B · 430 Å² buried · 4 hydrogen bonds · protein-protein

Compared structures

5WDR · Choanoflagellate Salpingoeca rosetta Ras with GMP-PNP · the same entry in another collection · chain A against A, TM-score 1.00

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 F2UBE5
Elsewhere: RCSB PDB 5WDR · PDBe 5WDR · UniProt F2UBE5

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