KpATCC43816 Protein target profile

excinuclease ABC subunit C

Accession: VK055_0033

Gene: uvrC AIK78664.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GQ96
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Length 610
Pocket druggability (P2Rank · AlphaFold DB model) 0.656
Functional annotation 0 EC 8 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. Second pocket predictor agrees P2Rank predicted binding-site probability 0.66. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 171 of 4744 screened genomes (3.6%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.66) — check the ligand evidence before deprioritizing on off-target risk alone. Weak predicted binding pocket FPocket selected-pocket score 0.30.

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
3.6% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
85.96 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) 0.656
Structure A0A0H3GQ96
Pocket Pocket 1
Druggability (FPocket) 0.303
Structure A0A0H3GQ96
Pocket Pocket 7
ColabFold model
P2Rank 0.621 · Pocket 1
FPocket 0.096 · Pocket 22
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 171 / 4744 genomes with a hit
Prevalence 3.6%

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.

MSDVFDAKAFLKTVTSQPGVYRMYDAGGTVIYVGKAKDLKKRLSSYFRSNLASRKTEALVALIAQIDVTVTHTETEALLLEHNYIKLYQPRYNVLLRDDKSYPFIFLSGDTHPRLAMHRGAKHAKGEYFGPFPNGYAVRETLALLQKIFPIRQCENSVYRNRSRPCLQYQIGRCLGPCVAGLVSEEEYAQQVEYVRLFLAGKDDQVLTQLIARMEKASQNLEFEEAARIRDQIQAVRRVTEKQFVSNTGDDLDVIGVAFDAGMACVHVLFIRQGKVLGSRSYFPKVPGGTELGEVVETFVGQFYLQGSQMRTLPGEILLDFNLGDKTLLADSLSELAGRRINVQTKPRGDRARYLKLARTNAATALTTKLSQQSTIHQRLQALASVLELPAVKRMECFDISHTMGEQTVASCVVFDSNGPLRAEYRRYNITGITPGDDYAAMNQVLRRRYGKAIDDNKIPDVILIDGGKGQLAQAKAVFAELDVPWDKHHPLLLGVAKGSDRKAGLETLFFEPEGEGFSLPPDSPALHVIQHIRDESHDHAISGHRKKRAKVKSTSSLETIEGVGPKRRQMLLKYMGGLQGLQQASVEEIAKVPGISHALAEKIFYSLKH

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

8
  • GO:0009380 Any of the protein complexes formed by the UvrABC excinuclease system, which carries out nucleotide excision repair. Three different complexes are formed by the 3 proteins as they proceed through the excision repair process. First a complex consisting of two A subunits and two B subunits bind DNA and unwind it around the damaged site. Then, the A subunits disassociate leaving behind a stable complex between B subunits and DNA. Now, subunit C binds to this B+DNA complex and causes subunit B to nick the DNA on one side of the complex while subunit C nicks the DNA on the other side of the complex. DNA polymerase I and DNA ligase can then repair the resulting gap.
  • GO:0005515 Binding to a protein.
  • GO:0006289 A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
  • 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:0009381 Catalysis of the hydrolysis of ester linkages within deoxyribonucleic acid at sites flanking regions of damaged DNA to which the Uvr ABC excinuclease complexes bind.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0009432 An error-prone process for repairing damaged microbial DNA.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

43 records
Show feature table
Start End DB Term Name
2 606 PANTHER PTHR30562 UVRC/OXIDOREDUCTASE
555 610 Gene3D G3DSA:1.10.150.20 -
588 607 SMART SM00278 HhH1_4
588 607 InterPro IPR003583 Helix-hairpin-helix DNA-binding motif, class 1
556 575 SMART SM00278 HhH1_4
556 575 InterPro IPR003583 Helix-hairpin-helix DNA-binding motif, class 1
548 608 FunFam G3DSA:1.10.150.20:FF:000005 UvrABC system protein C
5 102 Gene3D G3DSA:3.40.1440.10 -
5 102 InterPro IPR035901 GIY-YIG endonuclease superfamily
521 607 SUPERFAMILY SSF47781 RuvA domain 2-like
521 607 InterPro IPR010994 RuvA domain 2-like
204 239 ProSiteProfiles PS50151 UVR domain profile.
204 239 InterPro IPR001943 UVR domain
204 240 FunFam G3DSA:4.10.860.10:FF:000002 UvrABC system protein C
17 98 SMART SM00465 uri_9
17 98 InterPro IPR000305 GIY-YIG endonuclease
4 102 FunFam G3DSA:3.40.1440.10:FF:000001 UvrABC system protein C
377 552 Gene3D G3DSA:3.30.420.340 UvrC, RNAse H endonuclease domain
377 552 InterPro IPR038476 UvrC, RNAse H endonuclease domain superfamily
18 93 Pfam PF01541 GIY-YIG catalytic domain
18 93 InterPro IPR000305 GIY-YIG endonuclease
16 94 ProSiteProfiles PS50164 GIY-YIG domain profile.
16 94 InterPro IPR000305 GIY-YIG endonuclease
205 237 Pfam PF02151 UvrB/uvrC motif
205 237 InterPro IPR001943 UVR domain
378 549 FunFam G3DSA:3.30.420.340:FF:000001 UvrABC system protein C
190 243 SUPERFAMILY SSF46600 C-terminal UvrC-binding domain of UvrB
190 243 InterPro IPR036876 UVR domain superfamily
558 605 Pfam PF14520 Helix-hairpin-helix domain
9 589 NCBIfam TIGR00194 excinuclease ABC subunit UvrC
9 589 InterPro IPR004791 UvrABC system, subunit C
17 94 CDD cd10434 GIY-YIG_UvrC_Cho
17 94 InterPro IPR047296 UvrC/Cho-like, GIY-YIG domain
4 607 Hamap MF_00203 UvrABC system protein C [uvrC].
4 607 InterPro IPR004791 UvrABC system, subunit C
386 542 Pfam PF08459 UvrC RNAse H endonuclease domain
386 542 InterPro IPR001162 UvrC, RNAse H endonuclease domain
207 227 Coils Coil Coil
204 240 Gene3D G3DSA:4.10.860.10 UVR domain
254 479 ProSiteProfiles PS50165 UvrC family, homology region profile.
254 479 InterPro IPR001162 UvrC, RNAse H endonuclease domain
17 100 SUPERFAMILY SSF82771 GIY-YIG endonuclease
17 100 InterPro IPR035901 GIY-YIG endonuclease 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.

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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
0.656
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Surrounding area
Pocket 2 P2Rank #2
0.481
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Surrounding area
Pocket 3 P2Rank #3
0.03
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Surrounding area
Pocket 4 P2Rank #4
0.027
Likely same site as FPocket 7 0.6 Å 7 shared residues 88% of smaller site
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Surrounding area
Pocket 5 P2Rank #5
0.013
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Surrounding area

Binding pockets · FPocket

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

Pocket 1 FPocket #7
0.303
Likely same site as P2Rank 4 0.6 Å 7 shared residues 88% of smaller site
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_A0A0H3GQ96
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_0033
ColabFold — — full sequence — Loaded

Cross-references

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

Sequence

UniProt A0A0H3GQ96