Protein profile

KP13_02350

Ribosomal RNA large subunit methyltransferase M

Genome: KpKP13

Gene: AHE42920.1 rlmM Structure source: AlphaFold + ColabFold UniProt A0A0H3GXK1
Export view
Amino acids 366
Annotations 6
Features 17
PDB binders 1
Druggability 0.268

Overview

Basic information about this protein and its source genome.

Accession
KP13_02350
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE42920.1 rlmM
Status
annotated
Amino acids
366
Structure source
AlphaFold + ColabFold
EC
2.1.1.186
GO
GO:0032259 The process in which a methyl group is covalently attached to a molecule. GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0008757 Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate. GO:0006364 Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.

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 (%)
0.0
Localization
Cytoplasmic
ColabFold pLDDT
96.05

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 0.268
Structure A0A0H3GXK1
Pocket Pocket 23
P2Rank 0.094
Structure A0A0H3GXK1
Pocket Pocket 1
ColabFold model
FPocket 0.212 · Pocket 37
P2Rank 0.09 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 146 / 4744 genomes with a hit
Normalized 0.031

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0032259 The process in which a methyl group is covalently attached to a molecule.
  • GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0008757 Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a substrate.
  • GO:0006364 Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.

Sequence Features

Domain/signature hits from InterPro and related databases.

17 records
Show feature table
Start End DB Term Name
176 357 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
176 357 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
1 71 Pfam PF18125 RlmM ferredoxin-like domain
1 71 InterPro IPR040739 RlmM ferredoxin-like domain
1 360 PIRSF PIRSF028774 UCP028774
1 360 InterPro IPR011224 Ribosomal RNA large subunit methyltransferase M
80 175 FunFam G3DSA:3.30.2300.20:FF:000001 Ribosomal RNA large subunit methyltransferase M
176 357 FunFam G3DSA:3.40.50.150:FF:000020 Ribosomal RNA large subunit methyltransferase M
1 79 Gene3D G3DSA:3.30.70.2810 -
1 355 Hamap MF_01551 Ribosomal RNA large subunit methyltransferase M [rlmM].
1 355 InterPro IPR011224 Ribosomal RNA large subunit methyltransferase M
50 355 PANTHER PTHR37524 RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE M
186 279 Pfam PF01728 FtsJ-like methyltransferase
186 279 InterPro IPR002877 Ribosomal RNA methyltransferase, FtsJ domain
80 175 Gene3D G3DSA:3.30.2300.20 -
184 296 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
184 296 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...

Legend High Medium Low

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_A0A0H3GXK1
AlphaFold — — full sequence — Viewing
ColabFold KP13_02350
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
23 0.268

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 2.0 0.043
2 1.32 0.015

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.

16 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
TLA
4AUK
P0ADR6 150.1 Da LogP -2.12 TPSA 115.1 ✓ Ro5 ✓ Clean [C@@H]([C@H](C(=O)O)O)(C(=O)O)O

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.