Protein profile

KP13_02954

Ribosomal protein L11 methyltransferase

Genome: KpKP13

Gene: AHE42412.1 prmA Structure source: AlphaFold + ColabFold UniProt A0A0H3GWC1
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Amino acids 293
Annotations 7
Features 14
PDB binders 7
Druggability 0.985

Overview

Basic information about this protein and its source genome.

Accession
KP13_02954
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE42412.1 prmA
Status
annotated
Amino acids
293
Structure source
AlphaFold + ColabFold
EC
2.1.1.-
GO
GO:0008276 Catalysis of the transfer of a methyl group (CH3-) to a protein. GO:0006479 The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom. GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0005840 An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins. GO:0016279 Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the epsilon-amino group of a lysine residue in a protein substrate. 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
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
69.521
DEG E-value
2.4099999999999997e-152
Localization
Cytoplasmic
ColabFold pLDDT
86.92

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 0.985
Structure A0A0H3GWC1
Pocket Pocket 4
P2Rank 0.4
Structure A0A0H3GWC1
Pocket Pocket 1
ColabFold model
FPocket 0.716 · Pocket 1
P2Rank 0.419 · Pocket 1
Core conservation Accessory gene
Roary accessory
CoreCruncher accessory
Gut microbiome 172 / 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 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0008276 Catalysis of the transfer of a methyl group (CH3-) to a protein.
  • GO:0006479 The addition of a methyl group to a protein amino acid. A methyl group is derived from methane by the removal of a hydrogen atom.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0005840 An intracellular organelle, about 200 A in diameter, consisting of RNA and protein. It is the site of protein biosynthesis resulting from translation of messenger RNA (mRNA). It consists of two subunits, one large and one small, each containing only protein and RNA. Both the ribosome and its subunits are characterized by their sedimentation coefficients, expressed in Svedberg units (symbol: S). Hence, the prokaryotic ribosome (70S) comprises a large (50S) subunit and a small (30S) subunit, while the eukaryotic ribosome (80S) comprises a large (60S) subunit and a small (40S) subunit. Two sites on the ribosomal large subunit are involved in translation, namely the aminoacyl site (A site) and peptidyl site (P site). Ribosomes from prokaryotes, eukaryotes, mitochondria, and chloroplasts have characteristically distinct ribosomal proteins.
  • GO:0016279 Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the epsilon-amino group of a lysine residue in a protein substrate.
  • 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.

14 records
Show feature table
Start End DB Term Name
1 292 Hamap MF_00735 Ribosomal protein L11 methyltransferase [prmA].
1 292 InterPro IPR004498 Ribosomal protein L11 methyltransferase
3 292 Pfam PF06325 Ribosomal protein L11 methyltransferase (PrmA)
161 230 CDD cd02440 AdoMet_MTases
1 292 PANTHER PTHR43648 ELECTRON TRANSFER FLAVOPROTEIN BETA SUBUNIT LYSINE METHYLTRANSFERASE
1 293 PIRSF PIRSF000401 RPL11_MTase
1 293 InterPro IPR004498 Ribosomal protein L11 methyltransferase
101 293 Gene3D G3DSA:3.40.50.150 Vaccinia Virus protein VP39
101 293 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
44 291 SUPERFAMILY SSF53335 S-adenosyl-L-methionine-dependent methyltransferases
44 291 InterPro IPR029063 S-adenosyl-L-methionine-dependent methyltransferase superfamily
3 286 NCBIfam TIGR00406 50S ribosomal protein L11 methyltransferase
3 286 InterPro IPR004498 Ribosomal protein L11 methyltransferase
101 293 FunFam G3DSA:3.40.50.150:FF:000021 Ribosomal protein L11 methyltransferase

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_A0A0H3GWC1
AlphaFold — — full sequence — Viewing
ColabFold KP13_02954
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 0.985

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 4.34 0.181

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.

57 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
2MM
3CJQ
Q84BQ9 177.3 Da LogP 0.75 TPSA 40.5 ✓ Ro5 ✓ Clean CN(C)[C@@H](CCSC)C(=O)O
AZ8
5JE0
Q9LBJ0 165.1 Da LogP -1.60 TPSA 104.4 ✓ Ro5 ✓ Clean c1nc2c(nn1)NC(=O)NC2=O
AZ9
5JE5
Q9LBJ0 179.1 Da LogP -1.59 TPSA 93.5 ✓ Ro5 ✓ Clean CN1C(=O)c2c(nncn2)NC1=O
MEQ
1NV8
Q9WYV8 160.2 Da LogP -1.08 TPSA 92.4 ✓ Ro5 ✓ Clean CNC(=O)CC[C@@H](C(=O)O)N
PG0
6H2V
Q9NRN9 120.1 Da LogP -0.36 TPSA 38.7 ✓ Ro5 ✓ Clean COCCOCCO
SFG
2ZBR
Q84BQ9 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)…
TOF
5JDY
Q9LBJ0 193.2 Da LogP -1.63 TPSA 82.7 ✓ Ro5 ✓ Clean CN1C2=NC(=O)N(C(=O)C2=NC=N1)C

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.