Protein profile

KP13_03338

Ribosomal RNA large subunit methyltransferase H

Genome: KpKP13

Gene: rlmH AHE45717.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GJY6
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Amino acids 155
Annotations 5
Features 15
PDB binders 1
Druggability 0.411

Overview

Basic information about this protein and its source genome.

Accession
KP13_03338
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
rlmH AHE45717.1
Status
annotated
Amino acids
155
Structure source
AlphaFold + ColabFold
EC
2.1.1.177
GO
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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0070038 Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N3-methylpseudouridine.

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 (%)
94.839
DEG E-value
4.320000000000001e-109
Localization
Unknown
ColabFold pLDDT
96.47

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 0.411
Structure A0A0H3GJY6
Pocket Pocket 2
P2Rank 0.067
Structure A0A0H3GJY6
Pocket Pocket 1
ColabFold model
FPocket 0.639 · Pocket 1
P2Rank 0.103 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 169 / 4744 genomes with a hit
Normalized 0.036

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • 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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0070038 Catalysis of the reaction: S-adenosyl-L-methionine + rRNA = S-adenosyl-L-homocysteine + rRNA containing N3-methylpseudouridine.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records
Show feature table
Start End DB Term Name
1 154 PANTHER PTHR33603 METHYLTRANSFERASE
1 154 InterPro IPR003742 RNA methyltransferase RlmH
1 154 Hamap MF_00658 Ribosomal RNA large subunit methyltransferase H [rlmH].
1 153 SUPERFAMILY SSF75217 alpha/beta knot
1 153 InterPro IPR029028 Alpha/beta knot methyltransferases
3 154 CDD cd18081 RlmH-like
3 154 InterPro IPR003742 RNA methyltransferase RlmH
2 155 NCBIfam TIGR00246 23S rRNA (pseudouridine(1915)-N(3))-methyltransferase RlmH
2 155 InterPro IPR003742 RNA methyltransferase RlmH
1 153 Pfam PF02590 Predicted SPOUT methyltransferase
1 153 InterPro IPR003742 RNA methyltransferase RlmH
1 155 Gene3D G3DSA:3.40.1280.10 -
1 155 InterPro IPR029026 tRNA (guanine-N1-)-methyltransferase, N-terminal
1 154 PIRSF PIRSF004505 MT_bac
1 155 FunFam G3DSA:3.40.1280.10:FF:000004 Ribosomal RNA large subunit methyltransferase H

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_A0A0H3GJY6
AlphaFold — — full sequence — Viewing
ColabFold KP13_03338
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
2 0.411
1 0.335

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 1.39 0.017

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
SFG
5TWK
P0A8I8 381.4 Da LogP -2.06 TPSA 208.7 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…

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.