Protein profile

KP13_02425

30S ribosomal protein S16

Genome: KpKP13

Gene: AHE43139.1 rpsP Structure source: AlphaFold + ColabFold UniProt A0A0H3GS04
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Amino acids 82
Annotations 5
Features 16
PDB binders 6
Druggability 0.301

Overview

Basic information about this protein and its source genome.

Accession
KP13_02425
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE43139.1 rpsP
Status
annotated
Amino acids
82
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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0015935 The smaller of the two subunits of a ribosome.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
42.667
Human E-value
3.8e-18
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
90.244
DEG E-value
2.91e-50
Localization
Cytoplasmic
ColabFold pLDDT
95.88

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 0.301
Structure A0A0H3GS04
Pocket Pocket 2
P2Rank 0.019
Structure A0A0H3GS04
Pocket Pocket 1
ColabFold model
FPocket 0.149 · Pocket 2
P2Rank 0.031 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 1133 / 4744 genomes with a hit
Normalized 0.239

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • 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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0015935 The smaller of the two subunits of a ribosome.

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
75 82 Coils Coil Coil
1 82 FunFam G3DSA:3.30.1320.10:FF:000001 30S ribosomal protein S16
2 11 ProSitePatterns PS00732 Ribosomal protein S16 signature.
2 11 InterPro IPR020592 Ribosomal protein S16, conserved site
1 78 Hamap MF_00385 30S ribosomal protein S16 [rpsP].
1 78 InterPro IPR000307 Ribosomal protein S16
8 68 Pfam PF00886 Ribosomal protein S16
8 68 InterPro IPR000307 Ribosomal protein S16
1 81 Gene3D G3DSA:3.30.1320.10 -
1 81 InterPro IPR023803 Ribosomal protein S16 domain superfamily
2 79 NCBIfam TIGR00002 30S ribosomal protein S16
2 79 InterPro IPR000307 Ribosomal protein S16
1 79 PANTHER PTHR12919 30S RIBOSOMAL PROTEIN S16
1 79 InterPro IPR000307 Ribosomal protein S16
1 79 SUPERFAMILY SSF54565 Ribosomal protein S16
1 79 InterPro IPR023803 Ribosomal protein S16 domain 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

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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_A0A0H3GS04
AlphaFold — — full sequence — Viewing
ColabFold KP13_02425
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
2 0.301

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.

56 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
FES
6RW4
Q9Y3D3 175.8 Da LogP 1.29 TPSA 0.0 ✓ Ro5 ✓ Clean S1[Fe]S[Fe]1
GNP
6RW5
Q9Y3D3 522.2 Da LogP -2.76 TPSA 301.9 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O…
NMY
4LF6
Q5SJH3 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
Q5SJH3 286.4 Da LogP -3.55 TPSA 156.1 1 viol. ✓ Clean N[Os](N)(N)(N)(N)N
PAR
4DR2
Q5SJH3 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@…
SRY
6RW4
Q9Y3D3 581.6 Da LogP -7.74 TPSA 331.4 3 viol. ✓ Clean [H]/N=C(/N)\N[C@@H]1[C@H]([C@@H]([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.