KpATCC43816 Protein target profile

peptidyl-prolyl cis-trans isomerase

Accession: VK055_2524

Gene: AIK81121.1 surA 3D evidence: AlphaFold DB model + ColabFold model Metabolism 2 reactions UniProt A0A0H3GI34
Length 428
Pocket druggability (P2Rank · AlphaFold DB model) 0.769
Metabolic reactions 2
Chokepoint No
Direct ligand evidence 0 53 total records
Functional annotation 1 EC 7 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.

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
2.3% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
90.888 Higher values support similarity to known essential genes.
DEG E-value
0.0 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
89.32 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) 0.769
Structure A0A0H3GI34
Pocket Pocket 1
Druggability (FPocket) 0.5
Structure A0A0H3GI34
Pocket Pocket 21
ColabFold model
P2Rank 0.709 · Pocket 1
FPocket 0.507 · Pocket 25
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 110 / 4744 genomes with a hit
Prevalence 2.3%

Metabolic context

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

Explore metabolic network

Metabolic context: no human homolog detected.

Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Not a chokepoint
Pathways

No specific KEGG pathway assigned - this reaction either has no KEGG mapping, or only matches a generic overview map with no route-level information.

Catalyzed reactions

2 reactions mapped to this gene in the metabolic model. Open the full network to see each one, with substrates/products and the reaction-reaction map.

Imported from KpATCC43816.sbml · 2026-07-09

Sequence

Primary amino-acid sequence viewer.

MKNWKTLLLGIAMIANTSFAAPQVVDKVAAVVNNGVVLESDVDGLMQSVKLNAGQAGQQLPDDATLRHQILERLIMDQIVLQMGQKMGVKISDDQLDQAIANIAKQNNMTLDQMRSRLAYEGINYNTYRNQIRKEMLISEVRNNEVRRRITVLPQEVEALAKQIGDQNDASTELNLSHILIPLPENPTSDEVAAAQEQANSIVEQARNGANFGKLAITYSADQQALKGGQMGWGRIQELPGIFAQALSTAKKGDIVGPIRSGVGFHILKVNDLRGGTQNISVTEVHARHILLKPSPIMNDAQAQAKLEQIAAEIKSGKITFAQAAKTYSEDPGSANQGGDLGWATPDIFDPAFRDALMRLNKGQTSGPVHSSFGWHLIELLDSRQVDRTDAAQKDRAYRMLMNRKFSEEAATWMQEQRASAYVKILSN

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Subcellular localization

Localization
Periplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0003755 Catalysis of the reaction: peptidyl-proline (omega=180) = peptidyl-proline (omega=0).
  • GO:0050821 Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
  • GO:0006457 The process of assisting in the covalent and noncovalent assembly of single chain polypeptides or multisubunit complexes into the correct tertiary structure.
  • GO:0030288 The region between the inner (cytoplasmic or plasma) membrane and outer membrane of organisms with two membranes such as Gram negative bacteria. These periplasmic spaces are relatively thick and contain a thin peptidoglycan layer (PGL), also referred to as a thin cell wall.
  • GO:0051082 Binding to an unfolded protein.
  • GO:0042277 Binding to a peptide, an organic compound comprising two or more amino acids linked by peptide bonds.
  • GO:0043165 The assembly of an outer membrane of the type formed in Gram-negative bacteria. This membrane is enriched in polysaccharide and protein, and the outer leaflet of the membrane contains specific lipopolysaccharide structures.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

33 records
Show feature table
Start End DB Term Name
21 428 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
25 142 Pfam PF09312 SurA N-terminal domain
25 142 InterPro IPR015391 SurA N-terminal
283 384 SUPERFAMILY SSF54534 FKBP-like
382 428 Gene3D G3DSA:1.10.4030.10 -
21 148 FunFam G3DSA:1.10.4030.10:FF:000002 Chaperone SurA
1 20 SignalP_GRAM_NEGATIVE SignalP-noTM SignalP-noTM
280 381 FunFam G3DSA:3.10.50.40:FF:000007 Chaperone SurA
280 381 Gene3D G3DSA:3.10.50.40 -
280 381 InterPro IPR046357 Peptidyl-prolyl cis-trans isomerase domain superfamily
25 201 SUPERFAMILY SSF109998 Triger factor/SurA peptide-binding domain-like
25 201 InterPro IPR027304 Trigger factor/SurA domain superfamily
178 272 Pfam PF00639 PPIC-type PPIASE domain
178 272 InterPro IPR000297 Peptidyl-prolyl cis-trans isomerase, PpiC-type
173 275 SUPERFAMILY SSF54534 FKBP-like
282 382 ProSiteProfiles PS50198 PpiC-type peptidyl-prolyl cis-trans isomerase family profile.
282 382 InterPro IPR000297 Peptidyl-prolyl cis-trans isomerase, PpiC-type
1 20 Phobius SIGNAL_PEPTIDE Signal peptide region
7 15 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
16 20 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
321 342 ProSitePatterns PS01096 PpiC-type peptidyl-prolyl cis-trans isomerase signature.
321 342 InterPro IPR023058 Peptidyl-prolyl cis-trans isomerase, PpiC-type, conserved site
21 148 Gene3D G3DSA:1.10.4030.10 -
1 277 PANTHER PTHR47637 CHAPERONE SURA
171 272 ProSiteProfiles PS50198 PpiC-type peptidyl-prolyl cis-trans isomerase family profile.
171 272 InterPro IPR000297 Peptidyl-prolyl cis-trans isomerase, PpiC-type
1 20 SignalP_GRAM_POSITIVE SignalP-TM SignalP-TM
283 383 Pfam PF13616 PPIC-type PPIASE domain
163 279 Gene3D G3DSA:3.10.50.40 -
163 279 InterPro IPR046357 Peptidyl-prolyl cis-trans isomerase domain superfamily
1 6 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
9 428 Hamap MF_01183 Chaperone SurA [surA].
9 428 InterPro IPR023034 Peptidyl-prolyl isomerase SurA

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
0.769
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Surrounding area
Pocket 2 P2Rank #2
0.355
Likely same site as FPocket 15 0.8 Å 10 shared residues 100% of smaller site
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Surrounding area
Pocket 3 P2Rank #3
0.071
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Surrounding area
Pocket 4 P2Rank #4
0.041
Likely same site as FPocket 21 2.1 Å 11 shared residues 100% of smaller site
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Surrounding area
Pocket 5 P2Rank #5
0.035
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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 #21
0.5 Unusual size
Likely same site as P2Rank 4 2.1 Å 11 shared residues 100% of smaller site
Show in viewer
Surrounding area
Pocket 2 FPocket #15
0.35
Likely same site as P2Rank 2 0.8 Å 10 shared residues 100% of smaller site
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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_A0A0H3GI34
AlphaFold DB full sequence Viewing
ColabFold VK055_2524
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.

53 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 3 records from similar proteins
Structural ligands 3 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 50 similarity-based ZINC candidates
Best available ligand signal
2NV PDB via homolog 279.4 Da · LogP 0.44 · TPSA 72.2 Open detail RCSB PDB
D1D PDB via homolog Detail RCSB PDB
ICB PDB via homolog Detail RCSB PDB
ZINC142395 ZINC proposed compound · Tanimoto 0.700 Detail ZINC
ZINC141246167 ZINC proposed compound · Tanimoto 0.667 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
2NV RCSB PDB Q81CB1 279.4 Da LogP 0.44 TPSA 72.2 ✓ Ro5 ✓ Clean CCOCCOCCOCCOCCOC[C@@H](C)N
D1D RCSB PDB Q9Y237 152.2 Da LogP 0.10 TPSA 40.5 ✓ Ro5 ✓ Clean C1[C@H]([C@@H](CSS1)O)O
ICB RCSB PDB P56112 161.2 Da LogP 1.87 TPSA 53.1 ✓ Ro5 ✓ Clean c1ccc2c(c1)cc([nH]2)C(=O)O

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.