MolNFT v1 · #97843 · protein + RNA

Glycyl-tRNA synthetase in complex with tRNA-gly

4KR2 · Glycine--tRNA ligase: “Glycyl-tRNA synthetase in complex with tRNA-gly”. X-ray diffraction, 1 ligand (AMP), 9 pockets (best druggability 0.66). MolNFT v1 #97843 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4KR2
Type: protein + RNA
Length: 527 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycine--tRNA ligase; Gly-tRNA-ccc
EC: 6.1.1.14
UniProt: P41250
Ligands: AMP
Pockets: 9 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 29% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycine--tRNA ligase (EC 6.1.1.14)	protein	458	34% helix, 29% strand	P41250
C	Gly-tRNA-ccc	rna	69	—	—

Ligands and binding sites

AMP · Adenosine monophosphate · ligand · chains A

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	582	0.66	0.77	37	empty
2	384	0.66	0.80	29	empty
3	588	0.65	0.77	31	empty
4	333	0.63	0.79	48	AMP
5	89	0.45	0.80	23	empty

Interfaces

1 interface between chains.

A–C · 1446 Å² buried · 38 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

4KR2 · Glycyl-tRNA synthetase in complex with tRNA-Gly · the same entry in another collection · chain A against A, TM-score 1.00
P41250 · AlphaFold monomer V2.0 prediction for glycine--tRNA ligase (P41250) · a predicted model of the same protein · chain A 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 P41250
Elsewhere: RCSB PDB 4KR2 · PDBe 4KR2 · UniProt P41250

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