MolNFT v1 · #100972 · protein

Crystal structure of 3-nitro-tyrosine tRNA synthetase (5B) bound to 3- nitro-tyrosine

4NDA · Tyrosine--tRNA ligase: “Crystal structure of 3-nitro-tyrosine tRNA synthetase (5B) bound to 3- nitro-tyrosine”. X-ray diffraction, 2 ligands (NIY, NA), 1 pocket (best druggability 0.77). MolNFT v1 #100972 on GenesisL1: 3D structure…

PDB: 4NDA
Type: protein
Length: 308 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: NIY, NA
Pockets: 1 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 52% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosine--tRNA ligase (EC 6.1.1.1)	protein	308	52% helix, 13% strand	Q57834

Ligands and binding sites

NIY · Meta-nitro-tyrosine · ligand · chains A
NA · Sodium ion · metal · chains A
GOL · Glycerol · additive · 2 copies · 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	459	0.77	0.85	56	NIY, GOL

Compared structures

4NDA · Crystal structure of 3-nitro-tyrosine tRNA synthetase (5B) bound to 3-nitro-tyrosine · 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 0.99

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 4NDA · PDBe 4NDA · UniProt Q57834

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