Protein profile

VK055_2895

tRNA dimethylallyltransferase

Genome: KpATCC43816

Gene: miaA AIK81484.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GI16
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Amino acids 301
Annotations 5
Features 13
PDB binders 5
Druggability 0.939

Overview

Basic information about this protein and its source genome.

Accession
VK055_2895
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
miaA AIK81484.1
Status
annotated
Amino acids
301
Structure source
AlphaFold + ColabFold
EC
2.5.1.75
GO
GO:0008033 The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0052381 Catalysis of the reaction: adenosine(37) in tRNA + dimethylallyl diphosphate = N(6)-dimethylallyladenosine(37) in tRNA + diphosphate. 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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
40.196
Human E-value
2.44e-17
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
92.282
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
95.62

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 0.939
Structure A0A0H3GI16
Pocket Pocket 2
P2Rank 0.915
Structure A0A0H3GI16
Pocket Pocket 1
ColabFold model
FPocket 0.924 · Pocket 2
P2Rank 0.878 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 235 / 4744 genomes with a hit
Normalized 0.05

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0008033 The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0052381 Catalysis of the reaction: adenosine(37) in tRNA + dimethylallyl diphosphate = N(6)-dimethylallyladenosine(37) in tRNA + diphosphate.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

13 records
Show feature table
Start End DB Term Name
31 273 Pfam PF01715 IPP transferase
1 142 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
1 142 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
1 299 Gene3D G3DSA:3.40.50.300 -
1 299 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
105 175 Gene3D G3DSA:1.10.20.140 -
105 175 FunFam G3DSA:1.10.20.140:FF:000001 tRNA dimethylallyltransferase
1 294 PANTHER PTHR11088 TRNA DIMETHYLALLYLTRANSFERASE
1 294 InterPro IPR039657 Dimethylallyltransferase
1 294 Hamap MF_00185 tRNA dimethylallyltransferase [miaA].
1 294 InterPro IPR018022 IPP transferase
1 285 NCBIfam TIGR00174 tRNA (adenosine(37)-N6)-dimethylallyltransferase MiaA
1 285 InterPro IPR018022 IPP transferase

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

Loading 3D structure...

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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_A0A0H3GI16
AlphaFold — — full sequence — Viewing
ColabFold VK055_2895
ColabFold — — full sequence — Loaded
Pocket details FPocket · P2Rank — toggle visibility and zoom from here, or open full viewer

Pockets (FPOCKET)

Showing top-ranked FPocket candidates by druggability. Druggability is color-coded: high (0.7 or higher), medium (0.4 to 0.69), low (below 0.4).

FPOCKET Sticks Spheres Surfaces Druggability Labels Zoom Positions
2 0.939
3 0.226

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 16.82 0.788
2 16.38 0.778
3 1.2 0.01

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.

55 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
6IA
3EPL
P07884 417.4 Da LogP 0.01 TPSA 172.1 ✓ Ro5 ✓ Clean CC(C)CCNc1c2c(ncn1)n(cn2)[C@H]3[C@@H]([C@@H]([C…
DMA
3EPL
P07884 246.1 Da LogP 1.18 TPSA 113.3 ✓ Ro5 ✓ Clean CC(=CCO[P@@](=O)(O)OP(=O)(O)O)C
DPO
3CRQ
Q9HUL9 173.9 Da LogP -3.34 TPSA 135.6 ✓ Ro5 ✓ Clean [O-]P(=O)([O-])OP(=O)([O-])[O-]
DST
2ZXU
P16384 262.2 Da LogP 1.90 TPSA 104.1 ✓ Ro5 ✓ Clean CC(=CCS[P@@](=O)(O)OP(=O)(O)O)C
PPV
3EPH
P07884 178.0 Da LogP -0.81 TPSA 124.3 ✓ Ro5 ✓ Clean OP(=O)(O)OP(=O)(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.