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Crystal structure of tyrosine-tRNA ligase mutant complexed with unnatural amino acid 3-O-methyl-tyrosine

Analyse Crystal structure of tyrosine-tRNA ligase mutant complexed with unnatural amino… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4HPW
Type: protein
Length: 310 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosine--tRNA ligase
EC: 6.1.1.1
UniProt: Q57834
Ligands: 3YM
Pockets: 2 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 50% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosine--tRNA ligase (EC 6.1.1.1)	protein	310	50% helix, 13% strand	Q57834

Ligands and binding sites

3YM · 3-methoxy-L-tyrosine · ligand · chains A

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

Pockets

2 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	410	0.72	0.83	47	3YM
2	81	0.38	0.77	18	empty

Compared structures

4HPW · Crystal structure of Tyrosine-tRNA ligase mutant complexed with unnatural amino acid… · the same entry in another collection · chain A against A, TM-score 1.00
Q57834 · AlphaFold monomer V2.0 prediction for tyrosine--tRNA ligase (Q57834) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q57834
Elsewhere: RCSB PDB 4HPW · PDBe 4HPW · UniProt Q57834

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