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Crystal structure of T. cruzi histidyl-tRNA synthetase in complex with 4-chlorobenzene-1,2-diamine (chem 256)

Analyse Crystal structure of T. cruzi histidyl-tRNA synthetase in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YRJ
Type: protein
Length: 413 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Histidyl-tRNA synthetase
EC: 6.1.1.21
UniProt: Q4DA54
Ligands: HIS, 4JJ, SO4
Pockets: 4 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Histidyl-tRNA synthetase (EC 6.1.1.21)	protein	413	41% helix, 21% strand	Q4DA54

Ligands and binding sites

HIS · Histidine · ligand · chains A
4JJ · 4-chlorobenzene-1,2-diamine · ligand · chains A
SO4 · Sulfate ion · ion · 3 copies · chains A
DMS · Dimethyl sulfoxide · additive · 2 copies · chains A
EDO · 1,2-ethanediol · additive · chains A

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	580	0.72	0.80	55	HIS, 4JJ, SO4
2	106	0.57	0.85	25	empty
3	130	0.41	0.75	19	DMS
4	62	0.36	0.78	14	empty

Compared structures

4YRJ · Crystal structure of T. cruzi Histidyl-tRNA synthetase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q4DA54
Elsewhere: RCSB PDB 4YRJ · PDBe 4YRJ · UniProt Q4DA54

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