KpATCC43816 Protein target profile

elongation factor P (EF-P) OB domain protein

Accession: VK055_4918

Gene: AIK83444.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism Not in network UniProt A0A0H3GVI2
Length 190
Pocket druggability (FPocket · AlphaFold DB model) 0.021
Direct ligand evidence 0 51 total records
Functional annotation 0 EC 5 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.

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
2.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

Essential (DEG)
Y
DEG identity (%)
52.91 Higher values support similarity to known essential genes.
DEG E-value
1.15e-72 Smaller values mean stronger essential-gene similarity.

Structure confidence

ColabFold pLDDT
93.32 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)
Structure A0A0H3GVI2
Pocket No pockets
Druggability (FPocket) 0.021
Structure A0A0H3GVI2
Pocket Pocket 3
ColabFold model
FPocket 0.258 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 120 / 4744 genomes with a hit
Prevalence 2.5%

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.

MPRANEIKKGMVLNYNGKLLIVKNIDIQSPSARGAATLYKMRFSDVRTGLKVEERFKGDDIVDTVTLTRRFVDFSYVDGNEYVFMDKEDYTPYTFTKEQIEEELQFIPEGGMPDMQVLTWDGQLLALELPQTVDLEIIETAPGIKGASASSRTKPATMSTGLVIQVPEYLTTGEKIRIHIEECRYMGRAD

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Subcellular localization

Localization
Cytoplasmic

Gene Ontology (GO)

5
  • GO:0003746 Functions in chain elongation during polypeptide synthesis at the ribosome.
  • GO:0043043 The chemical reactions and pathways resulting in the formation of peptides, compounds of 2 or more (but usually less than 100) amino acids where the alpha carboxyl group of one is bound to the alpha amino group of another. This may include the translation of a precursor protein and its subsequent processing into a functional peptide.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0006414 The successive addition of amino acid residues to a nascent polypeptide chain during protein biosynthesis.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

37 records
Show feature table
Start End DB Term Name
1 65 SUPERFAMILY SSF50104 Translation proteins SH3-like domain
1 65 InterPro IPR008991 Translation protein SH3-like domain superfamily
66 130 FunFam G3DSA:2.40.50.140:FF:000053 Elongation factor P-like protein
1 64 FunFam G3DSA:2.30.30.30:FF:000011 Elongation factor P-like protein
72 124 Pfam PF01132 Elongation factor P (EF-P) OB domain
72 124 InterPro IPR001059 Translation elongation factor P/YeiP, central
133 188 SMART SM00841 Elong_fact_P_C_2
133 188 InterPro IPR015365 Elongation factor P, C-terminal
4 62 Pfam PF08207 Elongation factor P (EF-P) KOW-like domain
4 62 InterPro IPR013185 Translation elongation factor, KOW-like
1 64 Gene3D G3DSA:2.30.30.30 -
1 64 InterPro IPR014722 Ribosomal protein L2, domain 2
66 130 Gene3D G3DSA:2.40.50.140 -
66 130 InterPro IPR012340 Nucleic acid-binding, OB-fold
154 173 ProSitePatterns PS01275 Elongation factor P signature.
154 173 InterPro IPR013852 Translation elongation factor P/YeiP, conserved site
3 189 PANTHER PTHR30053 ELONGATION FACTOR P
3 189 InterPro IPR020599 Translation elongation factor P/YeiP
68 130 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
68 130 InterPro IPR012340 Nucleic acid-binding, OB-fold
2 189 Hamap MF_00646 Elongation factor P-like protein [yeiP].
2 189 InterPro IPR011897 Translation elongation factor P-like, YeiP
132 189 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
132 189 InterPro IPR012340 Nucleic acid-binding, OB-fold
133 188 CDD cd05794 S1_EF-P_repeat_2
132 190 Gene3D G3DSA:2.40.50.140 -
132 190 InterPro IPR012340 Nucleic acid-binding, OB-fold
69 125 SMART SM01185 EFP_2
69 125 InterPro IPR001059 Translation elongation factor P/YeiP, central
68 130 CDD cd04470 S1_EF-P_repeat_1
68 130 InterPro IPR001059 Translation elongation factor P/YeiP, central
1 190 PIRSF PIRSF005901 EF-P
1 190 InterPro IPR020599 Translation elongation factor P/YeiP
132 190 FunFam G3DSA:2.40.50.140:FF:000004 Elongation factor P
3 189 NCBIfam TIGR02178 elongation factor P-like protein YeiP
3 189 InterPro IPR011897 Translation elongation factor P-like, YeiP
133 188 Pfam PF09285 Elongation factor P, C-terminal

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
Residue sets
UniProt: Site:33-33 Probably interacts with 3' end of the P-site tRNA
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_A0A0H3GVI2
AlphaFold DB full sequence Viewing
ColabFold VK055_4918
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
KAA PDB via homolog 474.5 Da · LogP -3.14 · TPSA 243.8 Open detail RCSB PDB
ZINC168710640 ZINC proposed compound · Tanimoto 0.809 Detail ZINC
ZINC168710738 ZINC proposed compound · Tanimoto 0.809 Detail ZINC
ZINC1083817667 ZINC proposed compound · Tanimoto 0.768 Detail ZINC
ZINC936069053 ZINC proposed compound · Tanimoto 0.768 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
KAA RCSB PDB P0A6N4 474.5 Da LogP -3.14 TPSA 243.8 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…

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.