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Crystal structure of tryptophanyl-tRNA synthetase from vibrio cholerae with an endogenous tryptophan

Analyse Crystal structure of tryptophanyl-tRNA synthetase from vibrio cholerae with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3SZ3
Type: protein
Length: 341 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tryptophanyl-tRNA synthetase
EC: 6.1.1.2
UniProt: Q9KNV7
Ligands: TRP
Pockets: 1 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 57% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tryptophanyl-tRNA synthetase (EC 6.1.1.2)	protein	341	57% helix, 9% strand	Q9KNV7

Ligands and binding sites

TRP · Tryptophan · ligand · chains A
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	656	0.72	0.79	65	TRP

Compared structures

3SZ3 · Crystal structure of Tryptophanyl-tRNA synthetase from Vibrio cholerae with an endogenous… · the same entry in another collection · chain A against A, TM-score 1.00
Q9KNV7 · AlphaFold monomer V2.0 prediction for tryptophan--tRNA ligase (Q9KNV7) · 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 Q9KNV7
Elsewhere: RCSB PDB 3SZ3 · PDBe 3SZ3 · UniProt Q9KNV7

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