Protein profile

VK055_0112

23S rRNA m1G745 methyltransferase

Genome: KpATCC43816

Gene: AIK78740.1 yebH Structure source: AlphaFold + ColabFold UniProt A0A0H3GQ23
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Amino acids 264
Annotations 4
Features 11
PDB binders 1
Druggability 0.87

Overview

Basic information about this protein and its source genome.

Accession
VK055_0112
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK78740.1 yebH
Status
annotated
Amino acids
264
Structure source
AlphaFold + ColabFold
GO
GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule. GO:0046872 Binding to a metal ion. GO:0008757 Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate. GO:0032259 The process in which a methyl group is covalently attached to a molecule.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
33.673
Localization
Cytoplasmic
ColabFold pLDDT
93.47

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.87
Structure A0A0H3GQ23
Pocket Pocket 13
P2Rank 0.913
Structure A0A0H3GQ23
Pocket Pocket 1
ColabFold model
FPocket 0.989 · Pocket 1
P2Rank 0.895 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 117 / 4744 genomes with a hit
Normalized 0.025

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

4 GO

Gene Ontology (GO)

4
  • GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
  • GO:0046872 Binding to a metal ion.
  • GO:0008757 Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
  • GO:0032259 The process in which a methyl group is covalently attached to a molecule.

Sequence Features

Domain/signature hits from InterPro and related databases.

11 records
Show feature table
Start End DB Term Name
1 264 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
1 264 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
87 170 Pfam PF08241 Methyltransferase domain
87 170 InterPro IPR013216 Methyltransferase type 11
85 171 CDD cd02440 AdoMet_MTases
61 237 PANTHER PTHR43460 METHYLTRANSFERASE
1 263 PIRSF PIRSF018249 MyrA
1 263 InterPro IPR016718 rRNA (guanine-N1-)-methyltransferase A, predicted
1 264 FunFam G3DSA:3.40.50.150:FF:000163 23S rRNA methyltransferase A
4 246 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
4 246 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

3D visualization script Full viewer

Loading 3D structure...

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GQ23
AlphaFold — — full sequence — Viewing
ColabFold VK055_0112
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
13 0.87

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 20.2 0.851

Ligand evidence

Ligands grouped by evidence source. PDB ligands keep the source crystal visible, and loaded crystals can be opened directly in the structure viewer.

12 records

Structural evidence inferred from similar proteins. The source crystal indicates where the ligand was observed; the UniProt column identifies the homologous protein carrying that ligand.

Show only:
Ligand Source crystal UniProt (homolog) MW · LogP · TPSA Lipinski PAINS SMILES
TEX
5GM2
A0A077K7L1 437.6 Da LogP 4.85 TPSA 68.4 ✓ Ro5 Alert CC(C)[C@H]1C(=O)N[C@@H](Cc2c[nH]c3c2c(ccc3[C@](…

PDB and ChEMBL records on this protein are shown in full. ChEMBL records from similar proteins are capped at the top 100 per protein (by pchembl) and ZINC at the top 50 (Tanimoto ≥ 0.5). ADME columns are descriptor-based screening flags, not experimental toxicity results.