MolNFT v1 · #107863 · protein

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

4UP9 · Lysine--tRNA ligase: “Crystal structure of entamoeba histolytica lysyl-tRNA synthetase in complex with ATP”. X-ray diffraction, 1 ligand (ATP), 6 pockets (best druggability 0.74). MolNFT v1 #107863 on GenesisL1: 3D structure…

PDB: 4UP9
Type: protein
Length: 514 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: ATP
Pockets: 6 · best druggability 0.74

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	514	37% helix, 25% strand	C4M7X2

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · chains A

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

Pockets

6 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	769	0.74	0.79	67	ATP
2	264	0.61	0.80	39	empty
3	100	0.43	0.78	15	empty
4	104	0.37	0.74	18	empty
5	64	0.33	0.76	13	empty

Compared structures

4UP9 · Crystal structure of Entamoeba histolytica lysyl-tRNA synthetase in complex with ATP · 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 4UP9 · PDBe 4UP9 · UniProt C4M7X2

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