Protein profile

KP13_01427

Ribosomal RNA methyltransferase

Genome: KpKP13

Gene: AHE47405.1 grm Structure source: AlphaFold + ColabFold UniProt L7YCW5
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Amino acids 264
Annotations 4
Features 9
PDB binders 1
Druggability 0.987

Overview

Basic information about this protein and its source genome.

Accession
KP13_01427
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE47405.1 grm
Status
annotated
Amino acids
264
Structure source
AlphaFold + ColabFold
EC
2.1.1.179
GO
GO:0046677 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms. GO:0008649 Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a nucleoside residue in an rRNA molecule. The methyl group can be transfered to the nucleobase or to the ribose group of the nucleoside. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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
90.37

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 0.987
Structure L7YCW5
Pocket Pocket 1
P2Rank 0.877
Structure L7YCW5
Pocket Pocket 1
ColabFold model
FPocket 0.32 · Pocket 11
P2Rank 0.887 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 1 / 4744 genomes with a hit
Normalized 0

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 3 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

3
  • GO:0046677 Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an antibiotic stimulus. An antibiotic is a chemical substance produced by a microorganism which has the capacity to inhibit the growth of or to kill other microorganisms.
  • GO:0008649 Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to a nucleoside residue in an rRNA molecule. The methyl group can be transfered to the nucleobase or to the ribose group of the nucleoside.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Sequence Features

Domain/signature hits from InterPro and related databases.

9 records
Show feature table
Start End DB Term Name
11 244 Pfam PF07091 Ribosomal RNA methyltransferase (FmrO)
11 244 InterPro IPR025981 Ribosomal RNA aminoglycoside-resistance methyltransferase
2 249 PIRSF PIRSF015852 RRNA_mtase_Grm
2 249 InterPro IPR010769 Ribosomal RNA aminoglycoside-resistance methyltransferase, Gram-negative bacteria
58 248 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
58 248 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
3 55 Gene3D G3DSA:1.10.8.10 -
89 189 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
89 189 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_L7YCW5
AlphaFold — — full sequence — Viewing
ColabFold KP13_01427
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
1 0.987

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 15.46 0.754

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
5GP
3B89
Q763K9 363.2 Da LogP -2.57 TPSA 206.0 1 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)COP(=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.