KpATCC43816 Protein target profile

ribonuclease T2 family protein

Accession: VK055_1879

Gene: AIK80485.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GJX4
Length 265
Pocket druggability (P2Rank · AlphaFold DB model) 0.927
Direct ligand evidence 0 51 total records
Functional annotation 0 EC 3 GO
Target summary

Strong target candidate with converging metabolic, structural and chemical evidence.

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

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
1.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
N
DEG identity (%)
0.0 Higher values support similarity to known essential genes.

Structure confidence

ColabFold pLDDT
94.14 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) 0.927
Structure A0A0H3GJX4
Pocket Pocket 1
Druggability (FPocket) 0.778
Structure A0A0H3GJX4
Pocket Pocket 7
ColabFold model
P2Rank 0.922 · Pocket 1
FPocket 0.583 · Pocket 12
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 63 / 4744 genomes with a hit
Prevalence 1.3%

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.

MFRKDFAAIALVLTATQAGAEPLTATRYADFDRYVLALSWQTGFCQSMYDRNRNEPEECRLQQDTANKADFLTVHGLWPGLPKSIAARGVDERRWMRYGCATRPVPNMPEVKANRKCQAAETGLSLEMANKLNNVMPGSGGTSCLERYEYAKHGVCFGFDPDSYFGAMVRLNGEIKRSPVGDFLAKHYGQTVSRADFDAAVARAWGPQSVKAFKLTCNGNPAYLTEMQISLNAATINAPLATSAFLPQPHPGNCGAQFILDKVGH

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

3 GO

Subcellular localization

Localization
Periplasmic

Gene Ontology (GO)

3
  • GO:0033897 Catalysis of the reaction: a ribonucleotidyl-ribonucleotide-RNA + H2O = a 3'-end 3'-phospho-ribonucleotide-RNA + a 5'-end dephospho-ribonucleoside-RNA + H+. This reaction is a two-stage endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides with 2',3'-cyclic phosphate intermediates.
  • GO:0003723 Binding to an RNA molecule or a portion thereof.
  • GO:0006401 The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

19 records
Show feature table
Start End DB Term Name
1 20 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
1 20 Phobius SIGNAL_PEPTIDE Signal peptide region
21 265 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
1 5 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
72 79 ProSitePatterns PS00530 Ribonuclease T2 family histidine active site 1.
72 79 InterPro IPR018188 Ribonuclease T2, His active site 1
16 20 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
30 259 SUPERFAMILY SSF55895 Ribonuclease Rh-like
30 259 InterPro IPR036430 Ribonuclease T2-like superfamily
6 15 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
31 231 Pfam PF00445 Ribonuclease T2 family
31 231 InterPro IPR001568 Ribonuclease T2-like
19 234 PANTHER PTHR11240 RIBONUCLEASE T2
19 234 InterPro IPR001568 Ribonuclease T2-like
1 20 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
145 156 ProSitePatterns PS00531 Ribonuclease T2 family histidine active site 2.
145 156 InterPro IPR033130 Ribonuclease T2, His active site 2
23 265 Gene3D G3DSA:3.90.730.10 -
23 265 InterPro IPR036430 Ribonuclease T2-like superfamily

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.

Download VMD script Full viewer

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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 · P2Rank

Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Pocket 1 P2Rank #1
0.927
Likely same site as FPocket 7 6.7 Å 12 shared residues 100% of smaller site
Show in viewer
Surrounding area
Pocket 2 P2Rank #2
0.08
Show in viewer
Surrounding area
Pocket 3 P2Rank #3
0.031
Show in viewer
Surrounding area
Pocket 4 P2Rank #4
0.009
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #7
0.778
Likely same site as P2Rank 1 6.7 Å 12 shared residues 100% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #8
0.255
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_A0A0H3GJX4
AlphaFold DB full sequence Viewing
ColabFold VK055_1879
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.

51 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 1 records from similar proteins
Structural ligands 1 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
GPG PDB via homolog 628.5 Da · LogP -4.21 · TPSA 334.3 Open detail RCSB PDB
ZINC12501360 ZINC proposed compound · Tanimoto 0.794 Detail ZINC
ZINC104869865 ZINC proposed compound · Tanimoto 0.754 Detail ZINC
ZINC12504289 ZINC proposed compound · Tanimoto 0.754 Detail ZINC
ZINC34541308 ZINC proposed compound · Tanimoto 0.754 Detail ZINC

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
GPG RCSB PDB P21338 628.5 Da LogP -4.21 TPSA 334.3 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=…

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.