MolNFT v1 · #23669 · protein

Crystal structure of apo M. jannashii tyrosyl-tRNA synthetase

1U7D: “Crystal structure of apo M. jannashii tyrosyl-tRNA synthetase”. X-ray diffraction, 3 pockets (best druggability 0.70). MolNFT v1 #23669 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1U7D
Type: protein
Length: 576 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Tyrosyl-tRNA synthetase
EC: 6.1.1.1
UniProt: Q57834
Pockets: 3 · best druggability 0.70

Structure

x-ray diffraction · 2 distinct chains · 49% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Tyrosyl-tRNA synthetase (EC 6.1.1.1)	protein	292	51% helix, 13% strand	Q57834
B	Tyrosyl-tRNA synthetase (EC 6.1.1.1)	protein	284	47% helix, 14% strand	Q57834

Pockets

3 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	424	0.70	0.81	60	empty
2	380	0.66	0.79	48	empty
3	94	0.38	0.76	20	empty

Interfaces

1 interface between chains.

A–B · 1463 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

1U7D · crystal structure of apo M. jannashii tyrosyl-tRNA synthetase · the same entry in another collection · chain B against B, TM-score 1.00
Q57834 · AlphaFold monomer V2.0 prediction for tyrosine--tRNA ligase (Q57834) · 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 Q57834
Elsewhere: RCSB PDB 1U7D · PDBe 1U7D · UniProt Q57834

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