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The crystal structure of a human glycyl-tRNA synthetase mutant

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

PDB: 2PMF
Type: protein
Length: 522 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glycyl-tRNA synthetase
EC: 6.1.1.14
UniProt: P41250
Ligands: CL
Pockets: 6 · best druggability 0.72

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycyl-tRNA synthetase (EC 6.1.1.14)	protein	522	35% helix, 25% strand	P41250

Ligands and binding sites

CL · Chloride ion · ion · chains A
GOL · Glycerol · additive · chains A

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	951	0.72	0.76	64	empty
2	52	0.53	0.89	17	CL
3	102	0.37	0.75	20	empty
4	72	0.31	0.74	19	empty
5	55	0.30	0.75	16	empty

Compared structures

2PMF · The crystal structure of a human glycyl-tRNA synthetase mutant · 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 0.96

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 2PMF · PDBe 2PMF · UniProt P41250

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