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Crystal structure of human lysyl-tRNA synthetase Y145H mutant

Analyse Crystal structure of human lysyl-tRNA synthetase Y145H mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EA9
Type: protein
Length: 2,004 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lysine--tRNA ligase
EC: 2.7.7.-, 6.1.1.6
UniProt: Q15046
Ligands: KAA
Pockets: 20 · best druggability 0.83

Structure

x-ray diffraction · 3 distinct chains · 36% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Lysine--tRNA ligase (EC 2.7.7.-, 6.1.1.6)	protein	502	36% helix, 25% strand	Q15046
B	Lysine--tRNA ligase (EC 2.7.7.-, 6.1.1.6)	protein	500	36% helix, 26% strand	Q15046
D	Lysine--tRNA ligase (EC 2.7.7.-, 6.1.1.6)	protein	500	36% helix, 26% strand	Q15046

Ligands and binding sites

KAA · 5'-O-[(L-lysylamino)sulfonyl]adenosine · ligand · 4 copies · chains A, B, C, D
GOL · Glycerol · additive · 4 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	182	0.83	0.98	47	empty
2	180	0.82	0.97	49	empty
3	771	0.78	0.82	82	KAA, GOL
4	834	0.78	0.81	90	KAA, GOL
5	885	0.78	0.81	93	KAA, GOL

Interfaces

4 interfaces between chains.

C–D · 4366 Å² buried · 72 hydrogen bonds · protein-protein
A–B · 4341 Å² buried · 75 hydrogen bonds · protein-protein
B–D · 549 Å² buried · 5 hydrogen bonds · protein-protein
A–C · 28 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

7EA9 · Crystal Structure of human lysyl-tRNA synthetase Y145H mutant · 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 0.99

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 7EA9 · PDBe 7EA9 · UniProt Q15046

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