MolNFT v1 · #56871 · protein

Crystal structure of human glycyl-tRNA synthetase (glyrs) in complex with AP4A (cocrystallized with ATP)

2ZT5: “Crystal structure of human glycyl-tRNA synthetase (glyrs) in complex with AP4A (cocrystallized with ATP)”. X-ray diffraction, 1 ligand (B4P), 4 pockets (best druggability 0.81). MolNFT v1 #56871 on GenesisL1: 3D structure, binding…

PDB: 2ZT5
Type: protein
Length: 530 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: B4P
Pockets: 4 · best druggability 0.81

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glycyl-tRNA synthetase (EC 6.1.1.14)	protein	530	38% helix, 25% strand	P41250

Ligands and binding sites

B4P · Bis(adenosine)-5'-tetraphosphate · ligand · 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	1056	0.81	0.83	84	B4P
2	64	0.43	0.81	18	empty
3	86	0.37	0.76	27	empty
4	63	0.30	0.75	16	empty

Compared structures

2ZT5 · Crystal structure of human glycyl-trna synthetase (GLYRS) in complex with AP4A… · 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 0.91

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 2ZT5 · PDBe 2ZT5 · UniProt P41250

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