Protein target profile

VK055_3547

glycyl-tRNA synthetase, &beta subunit

Genome: KpATCC43816 Gene: glyS AIK82103.1 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3H4E2
Export view
Length 689
Pocket druggability 0.918
Metabolic reactions 1
Chokepoint No
Functional annotation 1 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. Structure available AlphaFold DB model + ColabFold model

Risks to review

Microbiome similarity 164 of 4744 screened genomes (3.5%) have a significant similarity hit. This target also has a predicted binding pocket (FPocket 0.92) — check the ligand evidence before deprioritizing on off-target risk alone. Best pocket may be a modeling artifact FPocket selected-pocket score 0.92, but this pocket's geometry is unusually large/diffuse compared to this protein's other predicted pockets — may reflect a low-confidence or disordered model region rather than a real cavity. Weak second pocket-predictor signal P2Rank predicted binding-site probability 0.19.

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
3.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Localization

Localization
Cytoplasmic

Structure confidence

ColabFold pLDDT
94.02 0-100 confidence; >70 supports local structural interpretation.

Binding-site evidence

AlphaFold DB / UniProt model

The selected pocket score is the FPocket value used for ranking after applying the curated structure priority. It estimates small-molecule pocket quality; it is not experimental binding evidence. The 3D viewer may show a different loaded structure, so visible pockets can differ.

FPocket 0.918
Structure A0A0H3H4E2
Pocket Pocket 1
P2Rank 0.19
Structure A0A0H3H4E2
Pocket Pocket 1
ColabFold model
FPocket 0.919 · Pocket 13
P2Rank 0.274 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 164 / 4744 genomes with a hit
Prevalence 3.5%

Cross-references

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

Sequence

UniProt A0A0H3H4E2

Pathways

KEGG R03654 BioCyc GLYCINE--TRNA-LIGASE-RXN

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
Aminoacyl-tRNA biosynthesis
Catalyzed reaction

1 reaction 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.

MSENTFLVEIGTEELPPKALRSLAESFAANVTAELDNAGLAHGKVEWFAAPRRLALKVANLAAAQADREVEKRGPAIAQAFDAEGKPSKAAEGWARGCGITVDQAERLTTDKGEWLLYRAHVKGESTEALLPNMIASSLAKLPIPKLMRWGASDVHFVRPVHTVTLLLGDKVIPATILGIPSDRVIRGHRFMGEPEFTIDHADQYPQILLERGKVIADYEQRKAKIKADAQEAARKIGGQADLSESLLEEVTSLVEWPVVLTAKFEEKFLAVPSEALVYTMKGDQKYFPVYDNAGKLLPNFIFVANIESKDPQQIISGNEKVVRPRLADAEFFFNTDRKKRLEDNLPRLETVLFQQQLGTLRDKTDRIQALAGWIAEQIGADVNHATRAGLLSKCDLMTNMVFEFTDTQGVMGMHYARHDGEAEDVAVALNEQYQPRFAGDALPSNPVACAVAIADKMDTLAGIFGIGQHPKGDKDPFALRRAALGVLRIIVEKNLDLDLQTLTEEAVRLYGEKLTNANVVDDVIDFMLGRFRAWYQDEGYGVDTIQAVLARRPTRPADFDARMKAVSHFRTLEESSALAAANKRVSNILAKSDETLNDIVHASVLKEAAEIKLAGNLVVLRDKLQPYFAAGRYQDALIELAALREPVDEFFENVMVNSEDKDVRINRLTLLSKLRELFLQVADISLLQ

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0004820 Catalysis of the reaction: ATP + glycine + tRNA(Gly) = AMP + diphosphate + glycyl-tRNA(Gly).
  • GO:0006426 The process of coupling glycine to glycyl-tRNA, catalyzed by glycyl-tRNA synthetase. The glycyll-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a glycine-accepting tRNA.
  • GO:0000166 Binding to a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
  • GO:0006420 The process of coupling arginine to arginyl-tRNA, catalyzed by arginyl-tRNA synthetase. The arginyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of an alanine accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
  • GO:0004814 Catalysis of the reaction: ATP + L-arginine + tRNA(Arg) = AMP + diphosphate + L-arginyl-tRNA(Arg).
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • 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.

24 records
Show feature table
Start End DB Term Name
216 236 Coils Coil Coil
318 334 PRINTS PR01045 Glycyl-tRNA synthetase beta subunit signature
318 334 InterPro IPR015944 Glycine-tRNA ligase, beta subunit
394 413 PRINTS PR01045 Glycyl-tRNA synthetase beta subunit signature
394 413 InterPro IPR015944 Glycine-tRNA ligase, beta subunit
50 62 PRINTS PR01045 Glycyl-tRNA synthetase beta subunit signature
50 62 InterPro IPR015944 Glycine-tRNA ligase, beta subunit
246 261 PRINTS PR01045 Glycyl-tRNA synthetase beta subunit signature
246 261 InterPro IPR015944 Glycine-tRNA ligase, beta subunit
7 20 PRINTS PR01045 Glycyl-tRNA synthetase beta subunit signature
7 20 InterPro IPR015944 Glycine-tRNA ligase, beta subunit
6 551 Pfam PF02092 Glycyl-tRNA synthetase beta subunit
6 551 InterPro IPR015944 Glycine-tRNA ligase, beta subunit
339 511 SUPERFAMILY SSF109604 HD-domain/PDEase-like
3 688 PANTHER PTHR30075 GLYCYL-TRNA SYNTHETASE
3 688 InterPro IPR006194 Glycine-tRNA synthetase, heterodimeric
363 653 ProSiteProfiles PS50861 Heterodimeric glycyl-transfer RNA synthetases family profile.
363 653 InterPro IPR006194 Glycine-tRNA synthetase, heterodimeric
5 688 NCBIfam TIGR00211 glycine--tRNA ligase subunit beta
5 688 InterPro IPR015944 Glycine-tRNA ligase, beta subunit
582 679 Pfam PF05746 DALR anticodon binding domain
582 679 InterPro IPR008909 DALR anticodon binding
3 688 Hamap MF_00255 Glycine--tRNA ligase beta subunit [glyS].
3 688 InterPro IPR015944 Glycine-tRNA ligase, beta subunit

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 · FPocket

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

Site 1 FPocket #1
0.918
Likely same site as P2Rank 5 2.7 Å 7 shared residues 100% of smaller site
Unusual size
Show in viewer
Surrounding area

Binding pockets · P2Rank

Probability: high ≥ 0.5 · medium 0.2–0.49 · low < 0.2

Site 1 P2Rank #1
0.19
Show in viewer
Surrounding area
Site 2 P2Rank #2
0.016
Show in viewer
Surrounding area
Site 3 P2Rank #3
0.009
Show in viewer
Surrounding area
Site 4 P2Rank #4
0.004
Show in viewer
Surrounding area
Site 5 P2Rank #5
0.002
Likely same site as FPocket 1 2.7 Å 7 shared residues 100% 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_A0A0H3H4E2
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_3547
ColabFold — — full sequence — Loaded