Protein profile

KP13_03996

50S ribosomal protein L13

Genome: KpKP13

Gene: rplM AHE42452.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GW96
Export view
Amino acids 142
Annotations 6
Features 19
PDB binders 5
Druggability 0.338

Overview

Basic information about this protein and its source genome.

Accession
KP13_03996
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
rplM AHE42452.1
Status
annotated
Amino acids
142
Structure source
AlphaFold + ColabFold
GO
GO:0003735 The action of a molecule that contributes to the structural integrity of the ribosome. 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:0006412 The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome. GO:0022625 The large subunit of a ribosome located in the cytosol. GO:0003729 Binding to messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns. GO:0017148 Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
37.0
Human E-value
1.84e-19
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
96.479
DEG E-value
4.06e-101
Localization
Cytoplasmic
ColabFold pLDDT
95.29

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 0.338
Structure A0A0H3GW96
Pocket Pocket 4
P2Rank 0.055
Structure A0A0H3GW96
Pocket Pocket 1
ColabFold model
FPocket 0.5 · Pocket 1
P2Rank 0.021 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 3000 / 4744 genomes with a hit
Normalized 0.632

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Gene Ontology (GO)

6
  • GO:0003735 The action of a molecule that contributes to the structural integrity of the ribosome.
  • 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:0006412 The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
  • GO:0022625 The large subunit of a ribosome located in the cytosol.
  • GO:0003729 Binding to messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
  • GO:0017148 Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.

Sequence Features

Domain/signature hits from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
1 142 PIRSF PIRSF002181 RPL13p_RPL13Aa_RPL16e_RPL13o
1 142 InterPro IPR005822 Ribosomal protein L13
4 142 NCBIfam TIGR01066 50S ribosomal protein L13
4 142 InterPro IPR005823 Ribosomal protein L13, bacterial-type
15 128 CDD cd00392 Ribosomal_L13
15 128 InterPro IPR005822 Ribosomal protein L13
105 127 ProSitePatterns PS00783 Ribosomal protein L13 signature.
105 127 InterPro IPR023563 Ribosomal protein L13, conserved site
1 141 PANTHER PTHR11545 RIBOSOMAL PROTEIN L13
1 141 InterPro IPR005822 Ribosomal protein L13
13 131 Pfam PF00572 Ribosomal protein L13
13 131 InterPro IPR005822 Ribosomal protein L13
1 142 FunFam G3DSA:3.90.1180.10:FF:000001 50S ribosomal protein L13
1 142 Gene3D G3DSA:3.90.1180.10 Ribosomal protein L13
1 142 InterPro IPR036899 Ribosomal protein L13 superfamily
1 140 SUPERFAMILY SSF52161 Ribosomal protein L13
1 140 InterPro IPR036899 Ribosomal protein L13 superfamily
15 141 Hamap MF_01366 50S ribosomal protein L13 [rplM].
15 141 InterPro IPR005822 Ribosomal protein L13

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...

Legend High Medium Low

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_A0A0H3GW96
AlphaFold — — full sequence — Viewing
ColabFold KP13_03996
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 0.338

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.

55 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
NMY
4V9C
P0AA10 614.7 Da LogP -8.90 TPSA 353.1 3 viol. ✓ Clean C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]2[C@…
OHX
4V8E
P60488 286.4 Da LogP -3.55 TPSA 156.1 1 viol. ✓ Clean N[Os](N)(N)(N)(N)N
PAR
4WOI
P0AA10 615.6 Da LogP -8.86 TPSA 347.3 3 viol. ✓ Clean C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]2[C@…
SPD
5JVG
Q9RXY1 145.2 Da LogP -0.34 TPSA 64.1 ✓ Ro5 ✓ Clean C(CCNCCCN)CN
YMZ
5UMD
Q8IJZ7 378.3 Da LogP 4.45 TPSA 45.2 ✓ Ro5 ✓ Clean c1cc2c(cc(nc2c(c1)C(F)(F)F)C(F)(F)F)[C@H]([C@@H…

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.