Protein profile

VK055_1845

tRNA-i(6)A37 thiotransferase enzyme MiaB

Genome: KpATCC43816

Gene: miaB AIK80451.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GTZ6
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Amino acids 474
Annotations 10
Features 35
PDB binders 2
Druggability 0.045

Overview

Basic information about this protein and its source genome.

Accession
VK055_1845
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
miaB AIK80451.1
Status
annotated
Amino acids
474
Structure source
AlphaFold + ColabFold
EC
2.8.4.3
GO
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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
35.772
Human E-value
2.5400000000000002e-86
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
36.961
Localization
Cytoplasmic
ColabFold pLDDT
92.24

Selected Druggability evidence

AlphaFold / UniProt model

Selected Druggability is the FPocket score chosen for ranking using the curated structure priority. The 3D viewer may show a different loaded structure, so its visible pockets can differ.

FPocket 0.045
Structure A0A0H3GTZ6
Pocket Pocket 28
P2Rank 0.929
Structure A0A0H3GTZ6
Pocket Pocket 1
ColabFold model
FPocket 0.148 · Pocket 2
P2Rank 0.942 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 263 / 4744 genomes with a hit
Normalized 0.055

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 9 GO

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 Features

Domain/signature hits 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; predicted models typically cover the full protein.

3D visualization script Full viewer

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Structural evidence

0 + 2

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3GTZ6
AlphaFold — — full sequence — Viewing
ColabFold VK055_1845
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (P2RANK)

Showing top-ranked P2Rank candidates by probability. Probability is color-coded per P2Rank calibration: high (≥ 0.5), medium (0.2 – 0.49), low (< 0.2).

P2RANK Sticks Spheres Surfaces Score Probability Labels Zoom Positions
1 23.17 0.887
2 3.76 0.145
3 0.87 0.003

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

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
2QGQ
Q9X2H6 221.3 Da LogP 1.19 TPSA 66.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NCCCS(=O)(=O)O
FS5
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.