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Crystal structure of entamoeba histolytica lysyl-tRNA synthetase in complex with lysyl-adenylate

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

PDB: 4UP7
Type: protein
Length: 529 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysine--tRNA ligase
EC: 6.1.1.6
UniProt: C4M7X2
Ligands: LAD
Pockets: 7 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine--tRNA ligase (EC 6.1.1.6)	protein	529	37% helix, 25% strand	C4M7X2

Ligands and binding sites

LAD · Adenosine-5'-[lysyl-phosphate] · ligand · chains A

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

Pockets

7 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	752	0.78	0.82	63	LAD
2	317	0.61	0.78	38	empty
3	68	0.37	0.77	12	empty
4	107	0.36	0.74	15	empty
5	68	0.34	0.76	14	empty

Compared structures

4UP7 · Crystal structure of Entamoeba histolytica lysyl-tRNA synthetase in complex with… · the same entry in another collection · chain A against A, TM-score 1.00

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 C4M7X2
Elsewhere: RCSB PDB 4UP7 · PDBe 4UP7 · UniProt C4M7X2

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