MolNFT v1 · #93305 · protein

Crystal structure of the RIO2 kinase-ADP/MG2+-phosphoaspartate complex from chaetomium thermophilum

4GYI: “Crystal structure of the RIO2 kinase-ADP/MG2+-phosphoaspartate complex from chaetomium thermophilum”. X-ray diffraction, 2 ligands (ADP, MG), 4 pockets (best druggability 0.60). MolNFT v1 #93305 on GenesisL1: 3D structure, binding…

PDB: 4GYI
Type: protein
Length: 339 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RIO2 kinase
UniProt: G0S5R3
Ligands: ADP, MG
Pockets: 4 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RIO2 kinase	protein	339	40% helix, 20% strand	G0S5R3

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A
MG · Magnesium ion · metal · chains A
EDO · 1,2-ethanediol · additive · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	329	0.60	0.77	32	ADP, MG
2	177	0.49	0.77	20	empty
3	109	0.45	0.78	18	empty
4	92	0.34	0.74	13	empty

Modifications

Observed in the structure: 1 modified (phosphorylation).

Compared structures

4GYI · Crystal structure of the Rio2 kinase-ADP/Mg2+-phosphoaspartate complex from Chaetomium… · 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 G0S5R3
Elsewhere: RCSB PDB 4GYI · PDBe 4GYI · UniProt G0S5R3

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