MolNFT v1 · #94012 · protein

Crystal structure of F2YRS complexed with F2Y

4HJX · Tyrosine-tRNA ligase: “Crystal structure of F2YRS complexed with F2Y”. X-ray diffraction, 1 ligand (F2Y), 5 pockets (best druggability 0.80). MolNFT v1 #94012 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4HJX
Type: protein
Length: 612 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosine-tRNA ligase
UniProt: Q57834
Ligands: F2Y
Pockets: 5 · best druggability 0.80

Structure

x-ray diffraction · 1 distinct chain · 49% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Tyrosine-tRNA ligase	protein	306	49% helix, 14% strand	Q57834

Ligands and binding sites

F2Y · 3,5-difluoro-L-tyrosine · ligand · 2 copies · chains A, B

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

Pockets

5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	426	0.80	0.88	53	F2Y
2	410	0.79	0.88	52	F2Y
3	141	0.52	0.80	24	empty
4	100	0.40	0.76	18	empty
5	90	0.37	0.75	14	empty

Interfaces

1 interface between chains.

A–B · 1330 Å² buried · 11 hydrogen bonds · protein-protein

Compared structures

4HJX · Crystal structure of F2YRS complexed with F2Y · 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 B 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 Q57834
Elsewhere: RCSB PDB 4HJX · PDBe 4HJX · UniProt Q57834

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