KpATCC43816 Protein target profile

crossover junction endodeoxyribonuclease RuvC

Accession: VK055_0070

Gene: AIK78698.1 ruvC 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GVH0
Export view
Length 173
Pocket druggability (P2Rank · AlphaFold DB model) 0.198
Functional annotation 1 EC 9 GO
Target summary

Target candidate with partial support; inspect missing evidence before prioritizing.

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. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 208 of 4744 screened genomes (4.4%) have a significant similarity hit. Weak predicted binding pocket FPocket selected-pocket score 0.30. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.20.

Evidence gaps

No ligand evidence No experimental PDB ligands, measured ChEMBL bioactivity, or proposed ZINC compound records are available.
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
4.4% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
97.11 Higher values support similarity to known essential genes.
DEG E-value
4.08e-123 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
91.05 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) 0.198
Structure A0A0H3GVH0
Pocket Pocket 1
Druggability (FPocket) 0.304
Structure A0A0H3GVH0
Pocket Pocket 2
ColabFold model
P2Rank 0.227 · Pocket 1
FPocket 0.778 · Pocket 3
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 208 / 4744 genomes with a hit
Prevalence 4.4%

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.

MAIILGIDPGSRVTGYGVIRQVGRQLSYLGSGCIRTKVDDLPSRLKLIYAGVTEIITQFQPDYFAIEQVFMAKNADSALKLGQARGVAIVAATNQALPVFEYAARQVKQTVVGIGSAEKSQVQHMVRTLLKLPANPQADAADALAIAITHCHVSQNAAQISETRLNLARGRLR

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0003676 Binding to a nucleic acid.
  • GO:0008821 Catalysis of the endonucleolytic cleavage at a junction such as a reciprocal single-stranded crossover between two homologous DNA duplexes (Holliday junction).
  • GO:0004520 Catalysis of the cleavage of ester linkages within deoxyribonucleic acid by creating internal breaks.
  • GO:0006310 Any process in which a new genotype is formed by reassortment of genes resulting in gene combinations different from those that were present in the parents. In eukaryotes genetic recombination can occur by chromosome assortment, intrachromosomal recombination, or nonreciprocal interchromosomal recombination. Interchromosomal recombination occurs by crossing over. In bacteria it may occur by genetic transformation, conjugation, transduction, or F-duction.
  • GO:0006281 The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0048476 An endodeoxyribonuclease complex that resolves the 4-way DNA intermediates of a Holliday junction into two separate duplex DNA molecules. Can be branch-migration associated.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0000287 Binding to a magnesium (Mg) ion.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
2 153 Hamap MF_00034 Crossover junction endodeoxyribonuclease RuvC [ruvC].
2 153 InterPro IPR002176 Crossover junction endodeoxyribonuclease RuvC
113 147 ProSitePatterns PS01321 Crossover junction endodeoxyribonuclease ruvC signature.
113 147 InterPro IPR020563 Crossover junction endodeoxyribonuclease RuvC, magnesium-binding site
3 162 PANTHER PTHR30194 CROSSOVER JUNCTION ENDODEOXYRIBONUCLEASE RUVC
3 162 InterPro IPR002176 Crossover junction endodeoxyribonuclease RuvC
4 150 Pfam PF02075 Crossover junction endodeoxyribonuclease RuvC
4 150 InterPro IPR002176 Crossover junction endodeoxyribonuclease RuvC
5 18 PRINTS PR00696 Crossover junction endodeoxyribonuclease RUVC signature
5 18 InterPro IPR002176 Crossover junction endodeoxyribonuclease RuvC
61 77 PRINTS PR00696 Crossover junction endodeoxyribonuclease RUVC signature
61 77 InterPro IPR002176 Crossover junction endodeoxyribonuclease RuvC
107 126 PRINTS PR00696 Crossover junction endodeoxyribonuclease RUVC signature
107 126 InterPro IPR002176 Crossover junction endodeoxyribonuclease RuvC
138 150 PRINTS PR00696 Crossover junction endodeoxyribonuclease RUVC signature
138 150 InterPro IPR002176 Crossover junction endodeoxyribonuclease RuvC
83 99 PRINTS PR00696 Crossover junction endodeoxyribonuclease RUVC signature
83 99 InterPro IPR002176 Crossover junction endodeoxyribonuclease RuvC
3 156 SUPERFAMILY SSF53098 Ribonuclease H-like
3 156 InterPro IPR012337 Ribonuclease H-like superfamily
2 159 Gene3D G3DSA:3.30.420.10 -
2 159 InterPro IPR036397 Ribonuclease H superfamily
2 158 FunFam G3DSA:3.30.420.10:FF:000002 Crossover junction endodeoxyribonuclease RuvC
4 136 CDD cd16962 RuvC
4 136 InterPro IPR002176 Crossover junction endodeoxyribonuclease RuvC
4 157 NCBIfam TIGR00228 crossover junction endodeoxyribonuclease RuvC
4 157 InterPro IPR002176 Crossover junction endodeoxyribonuclease RuvC

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

Loading 3D structure...

Drag to rotate — click the view, then scroll to zoom.

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
0.198
Likely same site as FPocket 2 2.8 Å 7 shared residues 88% of smaller site
Show in viewer
Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #2
0.304
Likely same site as P2Rank 1 2.8 Å 7 shared residues 88% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #1
0.224
Show in viewer
Surrounding area
Pocket 3 FPocket #5
0.224
Show in viewer
Surrounding area
Residue sets
UniProt: Active site:139-139
UniProt: Active site:67-67
UniProt: Active site:8-8
UniProt: Binding site:139-139
UniProt: Binding site:67-67
UniProt: Binding site:8-8
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_A0A0H3GVH0
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_0070
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GVH0