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Crystal structure of tyrosyl-tRNA synthetase from aeropyrum pernix

Analyse Crystal structure of tyrosyl-tRNA synthetase from aeropyrum pernix in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2CYA
Type: protein
Length: 328 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosyl-tRNA synthetase
EC: 6.1.1.1
UniProt: Q9YA64
Ligands: SO4
Pockets: 3 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 56% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosyl-tRNA synthetase (EC 6.1.1.1)	protein	328	56% helix, 11% strand	Q9YA64

Ligands and binding sites

SO4 · Sulfate ion · ion · 4 copies · chains A

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

Pockets

3 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	355	0.67	0.81	39	SO4
2	138	0.54	0.81	26	empty
3	52	0.25	0.72	12	empty

Compared structures

2CYA · Crystal structure of tyrosyl-tRNA synthetase from Aeropyrum pernix · the same entry in another collection · chain A against A, TM-score 1.00
Q9YA64 · AlphaFold monomer V2.0 prediction for tyrosine--tRNA ligase (Q9YA64) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 Q9YA64
Elsewhere: RCSB PDB 2CYA · PDBe 2CYA · UniProt Q9YA64

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