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Crystal structure of apo 3-nitro-tyrosine tRNA synthetase (5B) in the open form

Analyse Crystal structure of apo 3-nitro-tyrosine tRNA synthetase (5B) in the open form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ND6
Type: protein
Length: 303 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
Pockets: 1 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosine-tRNA ligase (EC 6.1.1.1)	protein	303	51% helix, 14% strand	Q57834

Ligands and binding sites

GOL · Glycerol · additive · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	645	0.75	0.81	63	empty

Compared structures

4ND6 · Crystal structure of apo 3-nitro-tyrosine tRNA synthetase (5B) in the open form · 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 4ND6 · PDBe 4ND6 · UniProt Q57834

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