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Crystal structure of class I lysyl-tRNA synthetase

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

PDB: 1IRX
Type: protein
Length: 1,015 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysyl-tRNA synthetase
EC: 6.1.1.6
UniProt: O57963
Ligands: ZN
Pockets: 11 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 46% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysyl-tRNA synthetase (EC 6.1.1.6)	protein	507	48% helix, 10% strand	O57963
B	Lysyl-tRNA synthetase (EC 6.1.1.6)	protein	508	44% helix, 12% strand	O57963

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1140	0.75	0.77	85	empty
2	418	0.63	0.78	46	empty
3	289	0.60	0.78	30	empty
4	378	0.60	0.76	57	empty
5	258	0.57	0.78	29	empty

Interfaces

1 interface between chains.

A–B · 569 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

1IRX · Crystal structure of class I lysyl-tRNA synthetase · the same entry in another collection · chain A against A, TM-score 1.00
O57963 · AlphaFold monomer V2.0 prediction for lysine--tRNA ligase (O57963) · a predicted model of the same protein · 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 O57963
Elsewhere: RCSB PDB 1IRX · PDBe 1IRX · UniProt O57963

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