MolNFT v1 · #107864 · protein

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

4UPA · Lysine--tRNA ligase: “Crystal structure of entamoeba histolytica lysyl-tRNA synthetase in complex with amppnp”. X-ray diffraction, 1 ligand (ANP), 6 pockets (best druggability 0.76). MolNFT v1 #107864 on GenesisL1: 3D structure…

PDB: 4UPA
Type: protein
Length: 515 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: ANP
Pockets: 6 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine--tRNA ligase (EC 6.1.1.6)	protein	515	38% helix, 25% strand	C4M7X2

Ligands and binding sites

ANP · Phosphoaminophosphonic acid-adenylate ester · 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	845	0.76	0.80	68	ANP
2	246	0.60	0.80	36	empty
3	145	0.49	0.78	17	empty
4	67	0.35	0.77	13	empty
5	91	0.34	0.74	20	empty

Compared structures

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

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