Research workbench

Crystal structure of a C-terminally truncated cyt-18 protein

Analyse Crystal structure of a C-terminally truncated cyt-18 protein in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1Y42
Type: protein
Length: 370 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosyl-tRNA synthetase, mitochondrial
EC: 6.1.1.1
UniProt: P12063
Ligands: TYR
Pockets: 6 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain · 57% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
X	Tyrosyl-tRNA synthetase, mitochondrial (EC 6.1.1.1)	protein	370	57% helix, 10% strand	P12063

Ligands and binding sites

TYR · Tyrosine · ligand · chains X

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

Pockets

6 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	367	0.66	0.80	37	TYR
2	90	0.57	0.86	21	empty
3	159	0.47	0.76	22	empty
4	143	0.38	0.73	23	empty
5	71	0.31	0.74	14	empty

Compared structures

1Y42 · Crystal structure of a C-terminally truncated CYT-18 protein · the same entry in another collection · chain X against X, TM-score 1.00
P12063 · AlphaFold monomer V2.0 prediction for tyrosine--tRNA ligase, mitochondrial (P12063) · a predicted model of the same protein · chain X against A, TM-score 0.99

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 P12063
Elsewhere: RCSB PDB 1Y42 · PDBe 1Y42 · UniProt P12063

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