MolNFT v1 · #178173 · protein

Crystal structure of saccharomyces cerevisiae lysyl-tRNA synthetase

7F6W · Lysine--tRNA ligase: “Crystal structure of saccharomyces cerevisiae lysyl-tRNA synthetase”. X-ray diffraction, 1 ligand (KAA), 4 pockets (best druggability 0.77). MolNFT v1 #178173 on GenesisL1: 3D structure, binding sites and…

PDB: 7F6W
Type: protein
Length: 506 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: A0A6V8RZ07
Ligands: KAA
Pockets: 4 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lysine--tRNA ligase (EC 6.1.1.6)	protein	506	35% helix, 26% strand	A0A6V8RZ07

Ligands and binding sites

KAA · 5'-O-[(L-lysylamino)sulfonyl]adenosine · ligand · chains A
PG6 · 1-(2-methoxy-ethoxy)-2-{2-[2-(2-methoxy-ethoxy]-ethoxy}-ethane · additive · chains A

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

Pockets

4 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	667	0.77	0.82	63	KAA
2	81	0.36	0.76	18	empty
3	90	0.35	0.75	19	empty
4	61	0.28	0.73	15	empty

Compared structures

7F6W · Crystal structure of Saccharomyces cerevisiae lysyl-tRNA Synthetase · 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 A0A6V8RZ07
Elsewhere: RCSB PDB 7F6W · PDBe 7F6W · UniProt A0A6V8RZ07

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