MolNFT v1 · #104184 · protein

Crystal structure of arginyl-tRNA synthetase

4Q2Y · Arginine--tRNA ligase, cytoplasmic: “Crystal structure of arginyl-tRNA synthetase”. X-ray diffraction, 20 pockets (best druggability 0.74). MolNFT v1 #104184 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4Q2Y
Type: protein
Length: 1,142 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Arginine--tRNA ligase, cytoplasmic
EC: 6.1.1.19
UniProt: P54136
Pockets: 20 · best druggability 0.74

Structure

x-ray diffraction · 2 distinct chains · 51% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Arginine--tRNA ligase, cytoplasmic (EC 6.1.1.19)	protein	565	50% helix, 10% strand	P54136
B	Arginine--tRNA ligase, cytoplasmic (EC 6.1.1.19)	protein	577	52% helix, 11% strand	P54136

Pockets

20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	689	0.74	0.80	44	empty
2	332	0.68	0.82	43	empty
3	553	0.63	0.75	44	empty
4	301	0.63	0.80	41	empty
5	522	0.62	0.75	42	empty

Interfaces

1 interface between chains.

A–B · 1236 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

4Q2Y · Crystal structure of Arginyl-tRNA synthetase · the same entry in another collection · chain A against A, TM-score 1.00
P54136 · AlphaFold monomer V2.0 prediction for arginine--tRNA ligase, cytoplasmic (P54136) · 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 P54136
Elsewhere: RCSB PDB 4Q2Y · PDBe 4Q2Y · UniProt P54136

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.