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Crystal structure of a RAS-like protein from cryphonectria parasitica in complex with GDP

Analyse Crystal structure of a RAS-like protein from cryphonectria parasitica in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4KU4
Type: protein
Length: 342 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RAS-3 from cryphonectria parasitica
Ligands: GDP, MG
Pockets: 2 · best druggability 0.48

Structure

x-ray diffraction · 2 distinct chains · 40% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RAS-3 from cryphonectria parasitica	protein	171	41% helix, 24% strand	—
B	RAS-3 from cryphonectria parasitica	protein	171	40% helix, 24% strand	—

Ligands and binding sites

GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 3 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	212	0.48	0.75	29	GDP, MG
2	107	0.37	0.74	22	GDP

Interfaces

1 interface between chains.

A–B · 248 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4KU4 · Crystal Structure of a Ras-like Protein from Cryphonectria parasitica in Complex with GDP · 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
Elsewhere: RCSB PDB 4KU4 · PDBe 4KU4

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