Protein profile

PA1563

23S rRNA (cytidine(2498)-2'-O)-methyltransferase RlmM

Genome: NC_002516.2

Gene: rlmM PA1563 Structure source: AlphaFold UniProt Q9I3F4
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Amino acids 352
Annotations 6
Features 15
PDB binders 1
Druggability 0.345

Overview

Basic information about this protein and its source genome.

Accession
PA1563
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
rlmM PA1563
Status
annotated
Amino acids
352
Structure source
AlphaFold
EC
2.1.1.186
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0070677 Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing 2'-O-methylcytosine. GO:0006364 Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules. GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule. 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
Gut microbiome off-target
hit
Essential (DEG)
N
Localization
Cytoplasmic

Selected Druggability evidence

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 0.345
Structure –
Pocket –

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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0070677 Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing 2'-O-methylcytosine.
  • GO:0006364 Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
  • GO:0008168 Catalysis of the transfer of a methyl group to an acceptor molecule.
  • 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.

15 records
Show feature table
Start End DB Term Name
1 352 PIRSF PIRSF028774 UCP028774
1 352 InterPro IPR011224 Ribosomal RNA large subunit methyltransferase M
1 70 Pfam PF18125 RlmM ferredoxin-like domain
1 70 InterPro IPR040739 RlmM ferredoxin-like domain
1 74 Gene3D G3DSA:3.30.70.2810 -
1 350 Hamap MF_01551 Ribosomal RNA large subunit methyltransferase M [rlmM].
1 350 InterPro IPR011224 Ribosomal RNA large subunit methyltransferase M
79 171 Gene3D G3DSA:3.30.2300.20 -
172 352 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
172 352 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
52 349 PANTHER PTHR37524 RIBOSOMAL RNA LARGE SUBUNIT METHYLTRANSFERASE M
181 274 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
181 274 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
182 276 Pfam PF01728 FtsJ-like methyltransferase
182 276 InterPro IPR002877 Ribosomal RNA methyltransferase, FtsJ domain

3D Structure

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

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Structural evidence

0 + 1

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA1563
AlphaFold — — full sequence — Viewing
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
1 0.345
4 0.207

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.