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Crystal structure of trmd, a M1G37 tRNA methyltransferase with SAM- competitive compounds

Analyse Crystal structure of trmd, a M1G37 tRNA methyltransferase with SAM- competitive… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YPZ
Type: protein
Length: 236 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA (guanine-N(1)-)-methyltransferase
EC: 2.1.1.228
UniProt: P43912
Ligands: 4FL
Pockets: 1 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	TRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228)	protein	236	44% helix, 17% strand	P43912

Ligands and binding sites

4FL · 4-(1H-imidazol-2-yl)pyridine · ligand · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	103	0.50	0.81	25	4FL

Compared structures

4YPZ · Crystal structure of TrmD, a M1G37 tRNA Methyltransferase with SAM-competitive compounds · the same entry in another collection · chain A against A, TM-score 1.00
P43912 · AlphaFold monomer V2.0 prediction for tRNA (guanine-N(1)-)-methyltransferase (P43912) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P43912
Elsewhere: RCSB PDB 4YPZ · PDBe 4YPZ · UniProt P43912

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