Research workbench

m1A58 tRNA methyltransferase mutant - Y78A

Analyse m1A58 tRNA methyltransferase mutant - Y78A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5C0O
Type: protein
Length: 918 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.62
Source: Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)
Molecule: tRNA (adenine(58)-N(1))-methyltransferase TrmI
EC: 2.1.1.220
UniProt: Q8GBB2
Ligands: SAM, SO4
Pockets: 12 · best druggability 0.85

Structure

x-ray diffraction · resolution 2.62 · 4 distinct chains · 29% helix, 31% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	tRNA (adenine(58)-N(1))-methyltransferase TrmI (EC 2.1.1.220)	protein	238	29% helix, 33% strand	Q8GBB2
F	tRNA (adenine(58)-N(1))-methyltransferase TrmI (EC 2.1.1.220)	protein	232	24% helix, 31% strand	Q8GBB2
G	tRNA (adenine(58)-N(1))-methyltransferase TrmI (EC 2.1.1.220)	protein	237	31% helix, 29% strand	Q8GBB2
H	tRNA (adenine(58)-N(1))-methyltransferase TrmI (EC 2.1.1.220)	protein	211	34% helix, 30% strand	Q8GBB2

Ligands and binding sites

SAM · S-adenosylmethionine · ligand · 4 copies · chains E, F, G, H
SO4 · Sulfate ion · ion · chains F, H

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

Pockets

12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1048	0.85	0.85	105	empty
2	111	0.79	0.98	21	empty
3	125	0.78	0.97	26	empty
4	223	0.54	0.78	36	SAM
5	72	0.48	0.84	16	empty

Interfaces

6 interfaces between chains.

E–G · 2336 Å² buried · 48 hydrogen bonds · protein-protein
F–H · 2293 Å² buried · 43 hydrogen bonds · protein-protein
G–H · 785 Å² buried · 18 hydrogen bonds · protein-protein
E–F · 772 Å² buried · 14 hydrogen bonds · protein-protein
E–H · 188 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 covalent (covalent ligand).

Compared structures

5C0O · M1A58 tRNA methyltransferase mutant - Y78A · the same entry in another collection · chain H against H, TM-score 1.00
Q8GBB2 · AlphaFold monomer V2.0 prediction for tRNA (ADENINE(58)-N(1))-methyltransferase trmi… · a predicted model of the same protein · chain G 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 Q8GBB2
Elsewhere: RCSB PDB 5C0O · PDBe 5C0O · UniProt Q8GBB2

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