KpATCC43816 Protein target profile

ribosomal protein L6

Accession: VK055_3770

Gene: AIK82325.1 rplF 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GZ96
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Length 177
Pocket druggability (FPocket · AlphaFold DB model) 0.707
Direct ligand evidence 0 55 total records
Functional annotation 0 EC 6 GO
Target summary

Promising target candidate with multiple supporting evidence streams.

Automated synthesis of the evidence currently loaded. Review the underlying records before prioritizing this protein.

Main supporting evidence

No similar human protein detected The current BLAST sequence screen did not find a significant human match, lowering apparent off-target risk. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Strong predicted binding pocket FPocket selected-pocket score 0.71. This is a computational pocket signal, not binding validation. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Microbiome similarity 426 of 4744 screened genomes (9.0%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.71) — check the ligand evidence before deprioritizing on off-target risk alone.

Evidence coverage

Core evidence streams are available for this target.
Terms and data sources used on this page

PDB: experimentally determined structures from the Protein Data Bank. These are the strongest structural evidence, but may cover only part of the protein.

AlphaFold DB model: a precomputed predicted structure downloaded from AlphaFold Database/UniProt, not an experiment performed here.

ColabFold model: a predicted structure generated for this workspace; interpret it with coverage and confidence.

pLDDT: confidence score for predicted structures. High values support local geometry; low values mean the region should not drive pocket interpretation.

FPocket / P2Rank: software tools that predict possible ligand-binding pockets on a 3D structure. They are useful screening signals, not experimental validation.

Druggability: a pocket-based estimate of whether a small molecule could bind productively. It does not mean a drug already exists.

PDB ligand: a compound observed in an experimental structure. Direct same-protein records are stronger than homolog-transferred records.

ChEMBL: a public database of measured compound bioactivity. Direct entries are stronger than entries transferred from similar proteins.

ZINC: a purchasable-compound database. Here it marks proposed candidates from chemical similarity, not measured binders.

LigQ / LigQ_2: an internal Target pipeline step that gathers PDB, ChEMBL, and ZINC ligand evidence for each protein.

Off-target: sequence similarity to proteins we prefer not to hit, such as human proteins or beneficial gut microbiome proteins.

DEG: Database of Essential Genes. A match suggests the protein resembles genes known to be essential in other organisms.

Roary / CoreCruncher: pan-genome tools used to decide whether a gene is core across analyzed strains or accessory/strain-specific.

EC / GO: functional annotations: EC describes enzyme reactions; GO describes biological process, molecular function, or cellular component.

KEGG pathway: a curated metabolic route label used here to group reactions imported from the metabolic model.

Chokepoint: a metabolic reaction that is the only producer or consumer of a metabolite in the imported model.

Prioritization evidence

Selectivity, essentiality, structural confidence, conservation, and predicted binding-site evidence.

Off-target risk

Human off-target
No hit
Gut microbiome similarity
9.0% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
99.435 Higher values support similarity to known essential genes.
DEG E-value
2.75e-128 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
92.96 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

P2Rank's binding-site probability is the primary druggability signal shown across the app; FPocket's druggability score is shown alongside it for comparison. Both estimate small-molecule pocket quality after applying the curated structure priority — neither is experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

Druggability (P2Rank)
Structure A0A0H3GZ96
Pocket No pockets
Druggability (FPocket) 0.707
Structure A0A0H3GZ96
Pocket Pocket 1
ColabFold model
FPocket 0.655 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 426 / 4744 genomes with a hit
Prevalence 9.0%

Metabolic context

Reactions catalyzed, pathway membership, and centrality in the genome-scale metabolic network.

This protein is not associated with the imported metabolic network for this genome.

Browse the genome's metabolic network

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MSRVAKAPVVVPAGVDVKINGQVITIKGKNGELTRTLNDAVEVKHADNALTFGPRDGYADGWAQAGTARALLNSMVIGVTEGFTKKLQLVGVGYRAAVKGNVVNLALGFSHPVDHQLPAGITAECPTQTEIVLKGADKQVIGQVAADLRAYRRPEPYKGKGVRYADEVVRTKEAKKK

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

6 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

6
  • 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:0019843 Binding to a ribosomal RNA.
  • GO:0022625 The large subunit of a ribosome located in the cytosol.
  • GO:0002181 The chemical reactions and pathways resulting in the formation of a protein in the cytoplasm. This is a ribosome-mediated process in which the information in messenger RNA (mRNA) is used to specify the sequence of amino acids in the protein.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
83 177 SUPERFAMILY SSF56053 Ribosomal protein L6
83 177 InterPro IPR036789 Ribosomal protein L6, alpha-beta domain superfamily
2 176 NCBIfam TIGR03654 50S ribosomal protein L6
2 176 InterPro IPR019906 Ribosomal protein L6, bacterial-type
1 82 SUPERFAMILY SSF56053 Ribosomal protein L6
1 82 InterPro IPR036789 Ribosomal protein L6, alpha-beta domain superfamily
154 162 ProSitePatterns PS00525 Ribosomal protein L6 signature 1.
154 162 InterPro IPR002358 Ribosomal protein L6, conserved site
1 176 Hamap MF_01365_B 50S ribosomal protein L6 [rplF].
1 176 InterPro IPR019906 Ribosomal protein L6, bacterial-type
83 177 FunFam G3DSA:3.90.930.12:FF:000001 50S ribosomal protein L6
83 177 Gene3D G3DSA:3.90.930.12 -
1 82 Gene3D G3DSA:3.90.930.12 -
71 96 PRINTS PR00059 Ribosomal protein L6 signature
71 96 InterPro IPR019906 Ribosomal protein L6, bacterial-type
99 115 PRINTS PR00059 Ribosomal protein L6 signature
99 115 InterPro IPR019906 Ribosomal protein L6, bacterial-type
141 162 PRINTS PR00059 Ribosomal protein L6 signature
141 162 InterPro IPR019906 Ribosomal protein L6, bacterial-type
1 82 FunFam G3DSA:3.90.930.12:FF:000002 50S ribosomal protein L6
1 177 PIRSF PIRSF002162 RPL6p_RPL6a_RPL9e_RPL9o
1 177 InterPro IPR000702 Ribosomal protein L6
1 177 PANTHER PTHR11655 60S/50S RIBOSOMAL PROTEIN L6/L9
90 164 Pfam PF00347 Ribosomal protein L6
90 164 InterPro IPR020040 Ribosomal protein L6, alpha-beta domain
11 82 Pfam PF00347 Ribosomal protein L6
11 82 InterPro IPR020040 Ribosomal protein L6, alpha-beta domain

3D structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; AlphaFold DB and ColabFold models typically cover the full protein but remain computational predictions.

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Pocket score High Medium Low
How colors and pocket overlays are used
Uniform protein color marks the displayed model as a single molecular object.
Experimental PDB structures may be colored by chain to distinguish subunits or copies present in the file.
Pocket colors and alpha spheres are evidence overlays for predicted binding cavities; they are not alternative protein chains.
'Alpha spheres' is FPocket's own cavity-shape geometry, imported when available and aligned with the loaded structure.
'Pocket atoms'/'Predicted site atoms' show the pocket's residue atoms instead: P2Rank reports residues rather than alpha spheres, and FPocket falls back to this when alpha-sphere geometry is unavailable or doesn't align.
'No pocket geometry' means neither alpha spheres nor residue-position data could be found for that pocket; the layer just highlights the same residues as 'Nearby residues'.
Pocket details Inspect a specific pocket, or open the full viewer

Binding pockets · FPocket

Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4

Pocket 1 FPocket #1
0.707
Show in viewer
Surrounding area
All structural evidence 0 experimental · 2 predicted

Structural evidence

0 + 2

Experimental PDB entries plus predicted AlphaFold DB or ColabFold models. Click Switch to display a different loaded structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold DB AF_A0A0H3GZ96
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_3770
ColabFold — — full sequence — Loaded

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
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 5 records from similar proteins
Structural ligands 5 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
6UQ PDB via homolog 1406.3 Da · LogP 0.84 · TPSA 388.0 Open detail RCSB PDB
8UZ PDB via homolog Detail RCSB PDB
EVN PDB via homolog Detail RCSB PDB
OHX PDB via homolog Detail RCSB PDB
PAR PDB via homolog Detail RCSB PDB

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
6UQ RCSB PDB
5KCR
P0AG55 1406.3 Da LogP 0.84 TPSA 388.0 3 viol. ✓ Clean Cc1c(c(c(c(c1Cl)O)Cl)OC)C(=O)O[C@@H]2[C@H](O[C@…
8UZ RCSB PDB
5NDW
P05738 483.5 Da LogP -7.33 TPSA 288.4 2 viol. ✓ Clean C1[C@H]([C@@H]([C@H]([C@@H]([C@H]1N)O[C@@H]2[C@…
EVN RCSB PDB
5KCS
P0AG55 1631.4 Da LogP 1.26 TPSA 479.1 3 viol. ✓ Clean Cc1cc(cc(c1C(=O)O[C@@H]2CO[C@]3([C@H]4[C@H]2OCO…
OHX RCSB PDB
4V88
P05738 286.4 Da LogP -3.55 TPSA 156.1 1 viol. ✓ Clean N[Os](N)(N)(N)(N)N
PAR RCSB PDB
5NDV
P05738 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@…

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.

Cross-references

External database identifiers for this protein, its structures, ligands, and metabolic reactions.

Sequence

UniProt A0A0H3GZ96