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tRNA ligase

Analyse tRNA ligase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6N0V
Type: protein
Length: 790 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.502
Source: Chaetomium thermophilum (strain DSM 1495 / CBS 144.50 / IMI 039719)
Molecule: tRNA ligase
EC: 6.5.1.3
UniProt: G0S6G2
Ligands: MN
Pockets: 9 · best druggability 0.78

Structure

x-ray diffraction · resolution 2.502 · 1 distinct chain · 34% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	tRNA ligase (EC 6.5.1.3)	protein	395	34% helix, 24% strand	G0S6G2

Ligands and binding sites

MN · Manganese (II) ion · metal · 2 copies · chains A, B

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

Pockets

9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1061	0.78	0.80	110	empty
2	257	0.60	0.79	27	empty
3	341	0.59	0.76	34	empty
4	272	0.56	0.77	35	empty
5	230	0.54	0.77	27	empty

Interfaces

1 interface between chains.

A–B · 857 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 modified (nonstandard).

Compared structures

6N0V · TRNA LIGASE · the same entry in another collection · chain A against A, TM-score 1.00

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 G0S6G2
Elsewhere: RCSB PDB 6N0V · PDBe 6N0V · UniProt G0S6G2

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