Protein profile

VK055_4653

23S rRNA m2A2503 methyltransferase

Genome: KpATCC43816

Gene: rlmN AIK83187.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GW32
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Amino acids 388
Annotations 14
Features 22
PDB binders 1
Druggability 0.583

Overview

Basic information about this protein and its source genome.

Accession
VK055_4653
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
rlmN AIK83187.1
Status
annotated
Amino acids
388
Structure source
AlphaFold + ColabFold
EC
2.1.1.192
GO
GO:0006364 Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules. GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic. GO:0030488 The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule. GO:0008173 Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA molecule. GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms. GO:0070475 The addition of a methyl group to an atom in the nucleoside base portion of a nucleotide residue in an rRNA molecule.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
74.728
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
91.0

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 0.583
Structure A0A0H3GW32
Pocket Pocket 1
P2Rank 0.932
Structure A0A0H3GW32
Pocket Pocket 1
ColabFold model
FPocket 0.419 · Pocket 23
P2Rank 0.931 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 231 / 4744 genomes with a hit
Normalized 0.049

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 13 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

13
  • GO:0006364 Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
  • GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
  • GO:0030488 The posttranscriptional addition of methyl groups to specific residues in a tRNA molecule.
  • GO:0008173 Catalysis of the transfer of a methyl group from a donor to a nucleoside residue in an RNA molecule.
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • GO:0070475 The addition of a methyl group to an atom in the nucleoside base portion of a nucleotide residue in an rRNA molecule.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
  • GO:0046872 Binding to a metal ion.
  • GO:0070040 Catalysis of the reaction: adenosine2503 in 23S rRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2-methyladenosine2503 in 23S rRNA + 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-adenosyl-L-homocysteine.
  • GO:0019843 Binding to a ribosomal RNA.
  • GO:0002935 Catalysis of the reaction: adenosine37 in tRNA + 2 reduced [2Fe-2S]-[ferredoxin] + 2 S-adenosyl-L-methionine = 2-methyladenosine37 in tRNA + 5'-deoxyadenosine + L-methionine + 2 oxidized [2Fe-2S]-[ferredoxin] + S-adenosyl-L-homocysteine.
  • GO:0000049 Binding to a transfer RNA.

Sequence Features

Domain/signature hits from InterPro and related databases.

22 records
Show feature table
Start End DB Term Name
1 82 Gene3D G3DSA:1.10.150.530 -
18 373 SFLD SFLDG01062 methyltransferase (Class A)
128 328 CDD cd01335 Radical_SAM
15 382 PIRSF PIRSF006004 Cfr
15 382 InterPro IPR004383 Ribosomal RNA large subunit methyltransferase RlmN/Cfr
83 353 Gene3D G3DSA:3.20.20.70 Aldolase class I
83 353 InterPro IPR013785 Aldolase-type TIM barrel
83 364 FunFam G3DSA:3.20.20.70:FF:000008 Dual-specificity RNA methyltransferase RlmN
120 338 SUPERFAMILY SSF102114 Radical SAM enzymes
21 368 Hamap MF_01849 Dual-specificity RNA methyltransferase RlmN [rlmN].
21 368 InterPro IPR027492 Dual-specificity RNA methyltransferase RlmN
124 295 Pfam PF04055 Radical SAM superfamily
124 295 InterPro IPR007197 Radical SAM
115 354 ProSiteProfiles PS51918 Radical SAM core domain profile.
115 354 InterPro IPR007197 Radical SAM
18 373 NCBIfam TIGR00048 23S rRNA (adenine(2503)-C(2))-methyltransferase RlmN
18 373 InterPro IPR027492 Dual-specificity RNA methyltransferase RlmN
1 82 FunFam G3DSA:1.10.150.530:FF:000001 Dual-specificity RNA methyltransferase RlmN
18 373 SFLD SFLDF00275 adenosine C2 methyltransferase (RlmN-like)
18 373 InterPro IPR004383 Ribosomal RNA large subunit methyltransferase RlmN/Cfr
10 369 PANTHER PTHR30544 23S RRNA METHYLTRANSFERASE
10 369 InterPro IPR040072 Methyltransferase (Class A)

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

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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_A0A0H3GW32
AlphaFold — — full sequence — Viewing
ColabFold VK055_4653
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
21 0.142
3 0.019
7 0.002
17 0.0

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 35.26 0.932
2 11.45 0.528

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.

51 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
5AD
5HR6
P36979 251.2 Da LogP -0.95 TPSA 119.3 ✓ Ro5 ✓ Clean C[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c2ncnc3N)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.