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Crystal structure of tRNA G26 methyltransferase TRM1 in apo form from pyrococcus horikoshii

Analyse Crystal structure of tRNA G26 methyltransferase TRM1 in apo form from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2DUL
Type: protein
Length: 367 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: N(2),N(2)-dimethylguanosine tRNA methyltransferase
EC: 2.1.1.32
UniProt: O59493
Pockets: 1 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 28% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	N(2),N(2)-dimethylguanosine tRNA methyltransferase (EC 2.1.1.32)	protein	367	40% helix, 28% strand	O59493

Ligands and binding sites

GOL · Glycerol · additive · chains A

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	177	0.57	0.81	39	empty

Compared structures

2DUL · Crystal structure of tRNA G26 methyltransferase Trm1 in apo form from Pyrococcus… · the same entry in another collection · chain A against A, TM-score 1.00
O59493 · AlphaFold monomer V2.0 prediction for tRNA (GUANINE(26)-N(2))-dimethyltransferase (O59493) · a predicted model of the same protein · chain A against A, TM-score 0.99

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 O59493
Elsewhere: RCSB PDB 2DUL · PDBe 2DUL · UniProt O59493

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