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Crystal Structure of H. influenzae TrmD in complex with Compound 30

Analyse Crystal Structure of H. influenzae TrmD in complex with Compound 30 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 8APW
Type: protein
Length: 250 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.8
Source: Haemophilus influenzae
Molecule: tRNA (guanine-N(1)-)-methyltransferase
EC: 2.1.1.228
UniProt: A5UG04
Ligands: NL1
Pockets: 1 · best druggability 0.50

Structure

x-ray diffraction · resolution 1.8 · 1 distinct chain · 42% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	tRNA (guanine-N(1)-)-methyltransferase (EC 2.1.1.228)	protein	250	42% helix, 16% strand	A5UG04

Ligands and binding sites

NL1 · 1-[2-oxidanylidene-2-(piperidin-4-ylamino)ethyl]pyrrolo[2,3-b]pyridine-5-carboxamide · ligand · chains A
CIT · Citric acid · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	107	0.50	0.81	26	NL1

Compared structures

A5UG04 · AlphaFold monomer V2.0 prediction for tRNA (guanine-N(1)-)-methyltransferase (A5UG04) · a predicted model of the same protein · chain A against A, TM-score 0.95

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 A5UG04
Elsewhere: RCSB PDB 8APW · PDBe 8APW · UniProt A5UG04

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