MolNFT v1 · #58980 · protein

Crystal structure of tetrameric form of human lysyl-tRNA synthetase

3BJU: “Crystal structure of tetrameric form of human lysyl-tRNA synthetase”. X-ray diffraction, 3 ligands (LYS, ATP, CA), 20 pockets (best druggability 0.84). MolNFT v1 #58980 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3BJU
Type: protein
Length: 1,998 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysyl-tRNA synthetase
EC: 6.1.1.6
UniProt: Q15046
Ligands: LYS, ATP, CA
Pockets: 20 · best druggability 0.84

Structure

x-ray diffraction · 4 distinct chains · 36% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysyl-tRNA synthetase (EC 6.1.1.6)	protein	503	36% helix, 25% strand	Q15046
B	Lysyl-tRNA synthetase (EC 6.1.1.6)	protein	495	35% helix, 26% strand	Q15046
C	Lysyl-tRNA synthetase (EC 6.1.1.6)	protein	501	35% helix, 26% strand	Q15046
D	Lysyl-tRNA synthetase (EC 6.1.1.6)	protein	499	36% helix, 26% strand	Q15046

Ligands and binding sites

LYS · Lysine · ligand · 4 copies · chains A, B, C, D
ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B, C, D
CA · Calcium ion · metal · 12 copies · chains A, B, C, D

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	461	0.84	0.91	90	empty
2	450	0.82	0.89	71	empty
3	972	0.78	0.80	91	CA, LYS, ATP
4	920	0.78	0.80	98	CA, LYS, ATP
5	860	0.77	0.81	79	CA, LYS, ATP

Interfaces

3 interfaces between chains.

A–B · 4365 Å² buried · 66 hydrogen bonds · protein-protein
C–D · 4346 Å² buried · 71 hydrogen bonds · protein-protein
B–D · 529 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

3BJU · Crystal Structure of tetrameric form of human lysyl-tRNA synthetase · the same entry in another collection · chain D against D, TM-score 1.00
Q15046 · AlphaFold monomer V2.0 prediction for lysine--tRNA ligase (Q15046) · a predicted model of the same protein · chain B 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 Q15046
Elsewhere: RCSB PDB 3BJU · PDBe 3BJU · UniProt Q15046

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