Protein profile

KP13_00770

30S ribosomal protein S13

Genome: KpKP13

Gene: AHE42384.1 rpsM Structure source: AlphaFold + ColabFold UniProt A0A0H3GU10
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Amino acids 118
Annotations 9
Features 20
PDB binders 2
Druggability 0.348

Overview

Basic information about this protein and its source genome.

Accession
KP13_00770
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE42384.1 rpsM
Status
annotated
Amino acids
118
Structure source
AlphaFold + ColabFold
GO
GO:0003735 The action of a molecule that contributes to the structural integrity of the ribosome. GO:0003676 Binding to a nucleic acid. 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:0003723 Binding to an RNA molecule or a portion thereof. 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: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
hit
Human identity (%)
27.344
Human E-value
4.49e-06
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
92.373
DEG E-value
1.85e-76
Localization
Cytoplasmic
ColabFold pLDDT
91.57

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 0.348
Structure A0A0H3GU10
Pocket Pocket 1
P2Rank
Structure A0A0H3GU10
Pocket No pockets
ColabFold model
FPocket 0.111 · Pocket 3
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 3686 / 4744 genomes with a hit
Normalized 0.777

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

9 GO

Gene Ontology (GO)

9
  • GO:0003735 The action of a molecule that contributes to the structural integrity of the ribosome.
  • GO:0003676 Binding to a nucleic acid.
  • 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:0003723 Binding to an RNA molecule or a portion thereof.
  • 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0015935 The smaller of the two subunits of a ribosome.
  • GO:0019843 Binding to a ribosomal RNA.
  • GO:0000049 Binding to a transfer RNA.

Sequence Features

Domain/signature hits from InterPro and related databases.

20 records
Show feature table
Start End DB Term Name
3 114 NCBIfam TIGR03631 30S ribosomal protein S13
3 114 InterPro IPR019980 Ribosomal protein S13, bacterial-type
1 71 Gene3D G3DSA:1.10.8.50 -
94 118 MobiDBLite mobidb-lite consensus disorder prediction
1 118 Hamap MF_01315 30S ribosomal protein S13 [rpsM].
1 118 InterPro IPR001892 Ribosomal protein S13
2 110 PANTHER PTHR10871 30S RIBOSOMAL PROTEIN S13/40S RIBOSOMAL PROTEIN S18
72 118 FunFam G3DSA:4.10.910.10:FF:000001 30S ribosomal protein S13
1 118 PIRSF PIRSF002134 RPS13p_RPS13a_RPS18e_RPS13o
4 111 ProSiteProfiles PS50159 Ribosomal protein S13 family profile.
4 111 InterPro IPR001892 Ribosomal protein S13
2 114 SUPERFAMILY SSF46946 S13-like H2TH domain
2 114 InterPro IPR010979 Ribosomal protein S13-like, H2TH
1 71 FunFam G3DSA:1.10.8.50:FF:000001 30S ribosomal protein S13
3 108 Pfam PF00416 Ribosomal protein S13/S18
3 108 InterPro IPR001892 Ribosomal protein S13
87 100 ProSitePatterns PS00646 Ribosomal protein S13 signature.
87 100 InterPro IPR018269 Ribosomal protein S13, conserved site
72 118 Gene3D G3DSA:4.10.910.10 30s ribosomal protein s13, domain 2
72 118 InterPro IPR027437 30s ribosomal protein S13, C-terminal

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_A0A0H3GU10
AlphaFold — — full sequence — Viewing
ColabFold KP13_00770
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 0.348

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.

53 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
GCP
4V8Y
P0CX55 521.2 Da LogP -2.22 TPSA 289.9 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
OHX
4V8Y
P0CX55 286.4 Da LogP -3.55 TPSA 156.1 1 viol. ✓ Clean N[Os](N)(N)(N)(N)N

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.