Protein profile

KP13_00340

Ribosomal RNA small subunit methyltransferase D

Genome: KpKP13

Gene: AHE42248.1 rsmD Structure source: AlphaFold + ColabFold UniProt A0A0H3GWZ1
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Amino acids 198
Annotations 6
Features 15
PDB binders 1
Druggability 0.395

Overview

Basic information about this protein and its source genome.

Accession
KP13_00340
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE42248.1 rsmD
Status
annotated
Amino acids
198
Structure source
AlphaFold + ColabFold
EC
2.1.1.171
GO
GO:0003676 Binding to a nucleic acid. 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:0031167 The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule. GO:0052913 Catalysis of the reaction: S-adenosyl-L-methionine + guanosine(966) in 16S rRNA = N(2)-methylguanosine(966) in 16S rRNA + S-adenosyl-L-homocysteine.

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 (%)
82.828
DEG E-value
2.3800000000000003e-124
Localization
Unknown
ColabFold pLDDT
90.0

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 0.395
Structure A0A0H3GWZ1
Pocket Pocket 4
P2Rank 0.318
Structure A0A0H3GWZ1
Pocket Pocket 1
ColabFold model
FPocket 0.573 · Pocket 6
P2Rank 0.298 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 152 / 4744 genomes with a hit
Normalized 0.032

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:0003676 Binding to a nucleic acid.
  • 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:0031167 The posttranscriptional addition of methyl groups to specific residues in an rRNA molecule.
  • GO:0052913 Catalysis of the reaction: S-adenosyl-L-methionine + guanosine(966) in 16S rRNA = N(2)-methylguanosine(966) in 16S rRNA + S-adenosyl-L-homocysteine.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records
Show feature table
Start End DB Term Name
12 188 Pfam PF03602 Conserved hypothetical protein 95
1 190 NCBIfam TIGR00095 16S rRNA (guanine(966)-N(2))-methyltransferase RsmD
1 190 InterPro IPR004398 RNA methyltransferase, RsmD
1 198 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
1 198 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
3 194 PANTHER PTHR43542 METHYLTRANSFERASE
3 194 InterPro IPR004398 RNA methyltransferase, RsmD
124 130 ProSitePatterns PS00092 N-6 Adenine-specific DNA methylases signature.
124 130 InterPro IPR002052 DNA methylase, N-6 adenine-specific, conserved site
81 101 Coils Coil Coil
11 191 PIRSF PIRSF004553 Methylase_YhhF
11 191 InterPro IPR004398 RNA methyltransferase, RsmD
11 189 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
11 189 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
57 130 CDD cd02440 AdoMet_MTases

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_A0A0H3GWZ1
AlphaFold — — full sequence — Viewing
ColabFold KP13_00340
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
4 0.395

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 4.69 0.205

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
6M1C
I6XFS7 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.