Research workbench

Crystal structure of apo S581L glycyl-tRNA synthetase mutant

Analyse Crystal structure of apo S581L glycyl-tRNA synthetase mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2Q5I
Type: protein
Length: 528 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycyl-tRNA synthetase
EC: 6.1.1.14
UniProt: P41250
Ligands: SO4
Pockets: 7 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycyl-tRNA synthetase (EC 6.1.1.14)	protein	528	36% helix, 26% strand	P41250

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A

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

Pockets

7 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	836	0.76	0.80	64	empty
2	53	0.41	0.82	17	empty
3	109	0.41	0.76	16	empty
4	62	0.36	0.78	17	empty
5	56	0.35	0.79	11	empty

Compared structures

2Q5I · Crystal structure of apo S581L Glycyl-tRNA synthetase mutant · the same entry in another collection · chain A against A, TM-score 1.00
P41250 · AlphaFold monomer V2.0 prediction for glycine--tRNA ligase (P41250) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P41250
Elsewhere: RCSB PDB 2Q5I · PDBe 2Q5I · UniProt P41250

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.