KpATCC43816 Protein target profile
glycyl-radical enzyme activating family protein
Accession: VK055_1471
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
Risks to review
Evidence coverage
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
- 0.7% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.
Essentiality
- Essential (DEG)
- N
- DEG identity (%)
- 26.496 Higher values support similarity to known essential genes.
Structure confidence
- ColabFold pLDDT
- 91.92 0-100 confidence; >70 supports local structural interpretation.
Binding-site evidence
AlphaFold DB / UniProt modelP2Rank'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.
Sequence
Primary amino-acid sequence viewer.
MTLSAAPRISCEVIDTRADRARIFNLQRYSLNDGQGIRTVVFFKGCPHTCPWCANPESISPRIQTLRRESKCLRCTRCQQDVAECPSGAWEQIGRDVTLDNLLQEVLKDEVFFRASGGGVTLSGGEVLMQAGFAARFLQRLRQWGIRTAIETAGDSAFDRFLPVAEACNEVLFDFKIMEPERARSLLRMNQPRVLDNFRQLAARKINLIPRVPLIPGYTLNTDNFRQILAFLAPFALKEMHLLPFHQYGEPKYRLLGKPWTLASVKAPDEAEIQPYRVMAEAAGFHVTIGG
Functional annotations
Enzyme classification and Gene Ontology terms linked to this protein.
Subcellular localization
- Localization
- Cytoplasmic
Gene Ontology (GO)
7- GO:0003824 Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
- GO:0051539 Binding to a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
- GO:0016491 Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
- GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
- GO:0043365 Catalysis of the reaction: S-adenosyl-L-methionine + dihydroflavodoxin + [formate C-acetyltransferase]-glycine = 5'-deoxyadenosine + L-methionine + flavodoxin semiquinone + [formate C-acetyltransferase]-glycin-2-yl radical.
- GO:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
- GO:0046872 Binding to a metal ion.
Sequence domains and features
Domain and signature matches imported from InterPro and related databases.
Show feature table
| Start | End | DB | Term | Name |
|---|---|---|---|---|
| 68 | 291 | PIRSF | PIRSF000371 | PFLA_YjjW |
| 68 | 291 | InterPro | IPR012839 | Organic radical enzyme activase |
| 14 | 81 | PIRSF | PIRSF000371 | PFLA_YjjW |
| 14 | 81 | InterPro | IPR012839 | Organic radical enzyme activase |
| 34 | 55 | ProSitePatterns | PS01087 | Radical activating enzymes signature. |
| 34 | 55 | InterPro | IPR001989 | Radical-activating enzyme, conserved site |
| 74 | 281 | NCBIfam | TIGR02494 | glycyl-radical enzyme activating protein |
| 32 | 282 | ProSiteProfiles | PS51918 | Radical SAM core domain profile. |
| 32 | 282 | InterPro | IPR007197 | Radical SAM |
| 19 | 284 | PANTHER | PTHR30352 | PYRUVATE FORMATE-LYASE-ACTIVATING ENZYME |
| 19 | 284 | InterPro | IPR034457 | Organic radical-activating enzymes |
| 21 | 92 | SUPERFAMILY | SSF54862 | 4Fe-4S ferredoxins |
| 73 | 257 | SUPERFAMILY | SSF102114 | Radical SAM enzymes |
| 33 | 156 | Pfam | PF13353 | 4Fe-4S single cluster domain |
| 40 | 246 | CDD | cd01335 | Radical_SAM |
| 18 | 290 | SFLD | SFLDG01118 | activating enzymes, group 2 |
| 18 | 290 | InterPro | IPR040074 | BssD/PflA/YjjW |
| 40 | 221 | Pfam | PF04055 | Radical SAM superfamily |
| 40 | 221 | InterPro | IPR007197 | Radical SAM |
| 18 | 290 | SFLD | SFLDS00029 | Radical SAM |
| 18 | 290 | InterPro | IPR007197 | Radical SAM |
| 20 | 289 | Gene3D | G3DSA:3.20.20.70 | Aldolase class I |
| 20 | 289 | InterPro | IPR013785 | Aldolase-type TIM barrel |
| 63 | 95 | ProSiteProfiles | PS51379 | 4Fe-4S ferredoxin-type iron-sulfur binding domain profile. |
| 63 | 95 | InterPro | IPR017896 | 4Fe-4S ferredoxin-type, iron-sulphur binding 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.
How colors and pocket overlays are used
Pocket details Inspect a specific pocket, or open the full viewer
- Method
- -
- Score
- -
- Visible layer
- -
- Residues
- -
- Pocket properties
- -
Selecting a pocket opens its details and centers the viewer without clearing other active layers. Use Focus this pocket when you want to hide the rest; use Surface for the wider residue environment.
Binding pockets · P2Rank
Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
Binding pockets · P2Rank
Druggability (P2Rank): high ≥ 0.5 · medium 0.2–0.49 · low < 0.2
Binding pockets · FPocket
Druggability (FPocket): high ≥ 0.7 · medium 0.4–0.69 · low < 0.4
All structural evidence
Structural evidence
0 + 2Experimental 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_A0A0C7KGK4
|
AlphaFold DB | — | — | full sequence | — | Viewing |
|
ColabFold
VK055_1471
|
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.
Structural ligand evidence is available for this target.
Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in Target, use Open crystal to inspect it in the structure viewer.
No PDB structure with a co-crystallized ligand found for this exact protein.
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.
Experimental bioactivity from ChEMBL measured directly on this protein. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL bioactivity data found for this exact protein.
Bioactivity inferred from similar proteins in ChEMBL. Score = pchembl (−log Ki/IC₅₀; higher = more potent).
No ChEMBL hits found through similar proteins.
Proposed virtual-screening candidates from ZINC. Score = Tanimoto similarity to a known binder (0–1; higher = more similar).
No virtual-screening candidates for this protein.
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.