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Crystal structure of methionyl tRNA synthetase Y225A mutant from thermus thermophilus

Analyse Crystal structure of methionyl tRNA synthetase Y225A mutant from thermus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2D54
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: 3 · best druggability 0.67

Structure

x-ray diffraction · 1 distinct chain · 52% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Methionyl-tRNA synthetase (EC 6.1.1.10)	protein	500	52% 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

3 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	548	0.67	0.77	57	empty
2	53	0.35	0.79	19	empty
3	58	0.28	0.74	12	empty

Compared structures

2D54 · Crystal Structure of Methionyl tRNA Synthetase Y225A Mutant from Thermus Thermophilus · 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 2D54 · PDBe 2D54 · UniProt P23395

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