Research workbench

Lysyl-tRNA synthetase (lyss) complexed with lysine

Analyse Lysyl-tRNA synthetase (lyss) complexed with lysine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1BBU
Type: protein
Length: 486 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (lysyl-tRNA synthetase)
EC: 6.1.1.6
UniProt: P0A8N3
Ligands: LYS
Pockets: 5 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 37% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protein (lysyl-tRNA synthetase) (EC 6.1.1.6)	protein	486	37% helix, 27% strand	P0A8N3

Ligands and binding sites

LYS · Lysine · ligand · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	608	0.73	0.81	60	LYS
2	101	0.41	0.77	18	empty
3	91	0.33	0.73	20	empty
4	56	0.31	0.76	17	empty
5	50	0.24	0.73	11	empty

Compared structures

1BBU · Lysyl-tRNA synthetase (lyss) complexed with lysine · the same entry in another collection · chain A against A, TM-score 1.00
P0A8N3 · AlphaFold monomer V2.0 prediction for lysine--tRNA ligase (P0A8N3) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P0A8N3
Elsewhere: RCSB PDB 1BBU · PDBe 1BBU · UniProt P0A8N3

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