Research workbench

Crystal structure of thermus thermophilus methionyl tRNA synthetase Y225F mutant obtained in the presence of PEG6000

Analyse Crystal structure of thermus thermophilus methionyl tRNA synthetase Y225F… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2D5B
Type: protein
Length: 500 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Methionyl-tRNA synthetase
EC: 6.1.1.10
UniProt: P23395
Ligands: ZN
Pockets: 2 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methionyl-tRNA synthetase (EC 6.1.1.10)	protein	500	51% helix, 16% strand	P23395

Ligands and binding sites

ZN · Zinc ion · metal · chains A

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

Pockets

2 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	573	0.69	0.78	74	empty
2	51	0.27	0.74	13	empty

Compared structures

2D5B · Crystal Structure of Thermus Thermophilus Methionyl tRNA synthetase Y225F Mutant obtained… · the same entry in another collection · chain A against A, TM-score 1.00
P23395 · AlphaFold monomer V2.0 prediction for methionine--tRNA ligase (P23395) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P23395
Elsewhere: RCSB PDB 2D5B · PDBe 2D5B · UniProt P23395

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