Protein profile

VK055_3848

30S ribosomal subunit protein S9

Genome: KpATCC43816

Gene: rpsI AIK82398.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GY63
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Amino acids 130
Annotations 5
Features 13
PDB binders 6
Druggability 0.422

Overview

Basic information about this protein and its source genome.

Accession
VK055_3848
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
rpsI AIK82398.1
Status
annotated
Amino acids
130
Structure source
AlphaFold + ColabFold
GO
GO:0003735 The action of a molecule that contributes to the structural integrity of the ribosome. 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: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:0022627 The small subunit of a ribosome located in the cytosol. GO:0003723 Binding to an RNA molecule or a portion thereof.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
39.024
Human E-value
9.54e-16
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
100.0
DEG E-value
5.22e-92
Localization
Cytoplasmic
ColabFold pLDDT
92.47

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 0.422
Structure A0A0H3GY63
Pocket Pocket 2
P2Rank
Structure A0A0H3GY63
Pocket No pockets
ColabFold model
FPocket 0.247 · Pocket 2
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 3506 / 4744 genomes with a hit
Normalized 0.739

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: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: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:0022627 The small subunit of a ribosome located in the cytosol.
  • GO:0003723 Binding to an RNA molecule or a portion thereof.

Sequence Features

Domain/signature hits from InterPro and related databases.

13 records
Show feature table
Start End DB Term Name
5 130 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like
5 130 InterPro IPR020568 Ribosomal protein S5 domain 2-type fold
1 130 Hamap MF_00532_B 30S ribosomal protein S9 [rpsI].
1 130 InterPro IPR023035 Ribosomal protein S9, bacterial/plastid
1 130 FunFam G3DSA:3.30.230.10:FF:000001 30S ribosomal protein S9
10 130 Pfam PF00380 Ribosomal protein S9/S16
10 130 InterPro IPR000754 Ribosomal protein S9
69 87 ProSitePatterns PS00360 Ribosomal protein S9 signature.
69 87 InterPro IPR020574 Ribosomal protein S9, conserved site
3 130 PANTHER PTHR21569 RIBOSOMAL PROTEIN S9
3 130 InterPro IPR000754 Ribosomal protein S9
1 130 Gene3D G3DSA:3.30.230.10 -
1 130 InterPro IPR014721 Ribosomal protein S5 domain 2-type fold, subgroup

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_A0A0H3GY63
AlphaFold — — full sequence — Viewing
ColabFold VK055_3848
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 0.422
11 0.02
3 0.002
6 0.001

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.

58 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
P0CX51 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
P0CX51 286.4 Da LogP -3.55 TPSA 156.1 1 viol. ✓ Clean N[Os](N)(N)(N)(N)N
PAR
4DR2
P80374 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@…
PCY
4KHP
P80374 558.6 Da LogP 0.75 TPSA 194.7 2 viol. ✓ Clean Cc1cccc(c1C(=O)OC[C@]2([C@H]([C@@H]([C@]([C@@]2…
TAC
1I97
P80374 444.4 Da LogP -0.21 TPSA 181.6 1 viol. ✓ Clean C[C@]1(c2cccc(c2C(=O)C3=C([C@]4([C@@H](C[C@@H]3…
WO2
1I97
P80374 — — — [O][W]1234O[W]567(O[W]89%10(O5[P]5%11O%12[W]%13…

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.