KpATCC43816 Protein target profile

tRNA-i(6)A37 thiotransferase enzyme MiaB

Accession: VK055_1845

Gene: AIK80451.1 miaB 3D evidence: AlphaFold DB model + ColabFold model Metabolism 1 reaction UniProt A0A0H3GTZ6
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Length 474
Pocket druggability (P2Rank · AlphaFold DB model) 0.929
Metabolic reactions 1
Chokepoint Yes
Direct ligand evidence 0 15 total records
Functional annotation 1 EC 9 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.

Main supporting evidence

Metabolic chokepoint Catalyzes a reaction that is the only producer or consumer of a metabolite in the imported metabolic model. Core gene across strains Marked as conserved by both pan-genome tools: Roary and CoreCruncher. Second pocket predictor agrees P2Rank predicted binding-site probability 0.93. Structure available AlphaFold DB model + ColabFold model Review the complete evidence below

Risks to review

Human similarity Top human hit identity: 35.772%. This target also has a predicted binding pocket (P2Rank 0.93) — check the ligand evidence before deprioritizing on off-target risk alone. Microbiome similarity 263 of 4744 screened genomes (5.5%) have a significant similarity hit. This target also has a predicted binding pocket (P2Rank 0.93) — check the ligand evidence before deprioritizing on off-target risk alone. Weak predicted binding pocket FPocket selected-pocket score 0.04.

Evidence coverage

Core evidence streams are available for this target.
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
Hit
Human identity (%)
35.772 Lower values reduce human off-target concern.
Human E-value
2.5400000000000002e-86
Gut microbiome similarity
5.5% of screened genomes Lower prevalence suggests narrower overlap with the screened gut microbiome.

Essentiality

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

Structure confidence

ColabFold pLDDT
92.24 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) 0.929
Structure A0A0H3GTZ6
Pocket Pocket 1
Druggability (FPocket) 0.045
Structure A0A0H3GTZ6
Pocket Pocket 28
ColabFold model
P2Rank 0.942 · Pocket 1
FPocket 0.148 · Pocket 2
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 263 / 4744 genomes with a hit
Prevalence 5.5%

Metabolic context

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

Explore metabolic network

Attractive metabolic target: catalyzes a consuming chokepoint reaction.

Relative network centrality 0.0% more central than 0.0% of genes in this genome
Chokepoint Chokepoint gene
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 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.

MTKKLHIKTWGCQMNEYDSSKMADLLDATHGYQLTEVAEEADVLLLNTCSIREKAQEKVFHQLGRWKLLKEKNPDLIIGVGGCVASQEGDHIRQRAHYVDIIFGPQTLHRLPEMINSVRGNRSPVVDISFPEIEKFDRLPEPRAEGPTAFVSIMEGCNKYCTYCVVPYTRGEEVSRPCDDILFEIAQLAAQGVREVNLLGQNVNAWRGENYDGTTGSFADLLRLVAAIDGIDRIRFTTSHPIEFTDDIIDVYRDTPELVSFLHLPVQSGSDRVLNLMGRTHTALEYKAIIRKLREARPDIQISSDFIVGFPGETTEDFEKTMKLIADVNFDMSYSFIFSARPGTPAADMVDDVPEADKKQRLYILQERINQQAMAWSRRMLGTVQRILVEGTSRKNIMELSGRTENNRVVNFEGTPDLVGKFVDVEIVDVYTNSLRGKIVRTEAEMGLRIAESPESVIARTRKENDLGVGIYQP

Functional annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

Subcellular localization

Localization
Cytoplasmic

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • 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:0035596 Catalysis of the addition of a methylthioether group (-SCH3) to a nucleic acid or protein acceptor.
  • GO:0016740 Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
  • 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:0006400 The covalent alteration of one or more nucleotides within a tRNA molecule to produce a tRNA molecule with a sequence that differs from that coded genetically.
  • GO:0051536 Binding to an iron-sulfur cluster, a combination of iron and sulfur atoms.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0046872 Binding to a metal ion.
  • GO:0035597 Catalysis of the reaction: N(6)-dimethylallyladenosine(37) in tRNA + [sulfur carrier]-SH + AH2 + 2 S-adenosyl-L-methionine = 2-methylsulfanyl-N(6)-dimethylallyladenosine(37) in tRNA + [sulfur carrier]-H + 5'-deoxyadenosine + L-methionine + A + S-adenosyl-L-homocysteine + 2 H+.

Sequence domains and features

Domain and signature matches imported from InterPro and related databases.

35 records
Show feature table
Start End DB Term Name
2 443 PANTHER PTHR43020 CDK5 REGULATORY SUBUNIT-ASSOCIATED PROTEIN 1
4 440 NCBIfam TIGR01574 tRNA (N6-isopentenyl adenosine(37)-C2)-methylthiotransferase MiaB
127 372 SUPERFAMILY SSF102114 Radical SAM enzymes
4 104 Pfam PF00919 Uncharacterized protein family UPF0004
4 104 InterPro IPR013848 Methylthiotransferase, N-terminal
2 443 SFLD SFLDS00029 Radical SAM
2 443 InterPro IPR007197 Radical SAM
143 375 ProSiteProfiles PS51918 Radical SAM core domain profile.
143 375 InterPro IPR007197 Radical SAM
3 120 ProSiteProfiles PS51449 Methylthiotransferase N-terminal domain profile.
3 120 InterPro IPR013848 Methylthiotransferase, N-terminal
66 366 SFLD SFLDG01082 B12-binding domain containing
2 443 SFLD SFLDF00273 (dimethylallyl)adenosine tRNA methylthiotransferase (MiaB-like)
2 443 InterPro IPR006463 tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase MiaB
3 440 Hamap MF_01864 tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase [miaB].
3 440 InterPro IPR006463 tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase MiaB
151 171 ProSitePatterns PS01278 Methylthiotransferase radical SAM domain signature.
151 171 InterPro IPR020612 Methylthiotransferase, conserved site
145 378 Gene3D G3DSA:3.80.30.20 tm_1862 like domain
145 378 InterPro IPR023404 Radical SAM, alpha/beta horseshoe
151 325 Pfam PF04055 Radical SAM superfamily
151 325 InterPro IPR007197 Radical SAM
147 367 SMART SM00729 MiaB
147 367 InterPro IPR006638 Elp3/MiaA/NifB-like, radical SAM core domain
4 437 NCBIfam TIGR00089 MiaB/RimO family radical SAM methylthiotransferase
4 437 InterPro IPR005839 Methylthiotransferase
3 129 Gene3D G3DSA:3.40.50.12160 -
3 129 InterPro IPR038135 Methylthiotransferase, N-terminal domain superfamily
378 441 ProSiteProfiles PS50926 TRAM domain profile.
378 441 InterPro IPR002792 TRAM domain
145 378 FunFam G3DSA:3.80.30.20:FF:000001 tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase 2
378 440 Pfam PF01938 TRAM domain
378 440 InterPro IPR002792 TRAM domain
156 357 CDD cd01335 Radical_SAM
3 130 FunFam G3DSA:3.40.50.12160:FF:000001 tRNA-2-methylthio-N(6)-dimethylallyladenosine synthase

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
0.929
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Surrounding area
Pocket 2 P2Rank #2
0.323
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Surrounding area
Pocket 3 P2Rank #3
0.047
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Surrounding area
Pocket 4 P2Rank #4
0.03
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Surrounding area
Pocket 5 P2Rank #5
0.028
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Surrounding area
Residue sets
UniProt: Binding site:12-12
UniProt: Binding site:157-157
UniProt: Binding site:161-161
UniProt: Binding site:164-164
UniProt: Binding site:49-49
UniProt: Binding site:83-83
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_A0A0H3GTZ6
AlphaFold DB — — full sequence — Viewing
ColabFold VK055_1845
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.

15 records
Chemistry signal

Structural ligand evidence is available for this target.

Direct evidence 0 same-protein records
Transferred evidence 2 records from similar proteins
Structural ligands 2 0 loaded crystals
Measured bioactivity 0 direct and transferred ChEMBL records
Proposed compounds 13 similarity-based ZINC candidates
Best available ligand signal
CXS PDB via homolog 221.3 Da · LogP 1.19 · TPSA 66.4 Open detail RCSB PDB
FS5 PDB via homolog Detail RCSB PDB
ZINC2004372 ZINC proposed compound · Tanimoto 1.000 Detail ZINC
ZINC38364153 ZINC proposed compound · Tanimoto 0.926 Detail ZINC
ZINC1710230 ZINC proposed compound · Tanimoto 0.786 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
CXS RCSB PDB
2QGQ
Q9X2H6 221.3 Da LogP 1.19 TPSA 66.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NCCCS(=O)(=O)O
FS5 RCSB PDB
4JC0
Q9X2H6 863.6 Da LogP 8.41 TPSA 0.0 2 viol. ✓ Clean S(SS[Fe]12[S]3[Fe]4[S]1[Fe]5[S]4[Fe]3[S]25)SS[F…

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.

Sequence

UniProt A0A0H3GTZ6

Pathways

BioCyc RXN0-5063