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Structure of yibk from haemophilus influenzae (HI0766): a methyltransferase with a cofactor bound at a site formed by a knot

Analyse Structure of yibk from haemophilus influenzae (HI0766): a methyltransferase… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1MXI
Type: protein
Length: 156 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hypothetical TRNA/RRNA methyltransferase HI0766
EC: 2.1.1.-
UniProt: P44868
Ligands: SAH, IOD
Pockets: 1 · best druggability 0.58

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Hypothetical TRNA/RRNA methyltransferase HI0766 (EC 2.1.1.-)	protein	156	35% helix, 17% strand	P44868

Ligands and binding sites

SAH · S-adenosyl-L-homocysteine · ligand · chains A
IOD · Iodide ion · ion · 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	145	0.58	0.83	24	SAH

Compared structures

1MXI · Structure of YibK from Haemophilus influenzae (HI0766): a Methyltransferase with a… · the same entry in another collection · chain A against A, TM-score 1.00
P44868 · AlphaFold monomer V2.0 prediction for tRNA (CYTIDINE(34)-2'-O)-methyltransferase (P44868) · a predicted model of the same protein · chain A against A, TM-score 0.97

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P44868
Elsewhere: RCSB PDB 1MXI · PDBe 1MXI · UniProt P44868

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