Protein profile

VK055_0276

threonine--tRNA ligase

Genome: KpATCC43816

Gene: AIK78902.1 thrS Structure source: AlphaFold + ColabFold UniProt A0A0H3GPK3
Amino acids 622
Annotations 8
Features 53
PDB binders 12
Druggability 0.204

Overview

Basic information about this protein and its source genome.

Accession
VK055_0276
Gene
AIK78902.1 thrS
Status
annotated
Amino acids
622
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
40.336
Human E-value
4.32e-88
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
96.302
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
96.14

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 0.204
Structure A0A0H3GPK3
Pocket Pocket 2
P2Rank 0.858
Structure A0A0H3GPK3
Pocket Pocket 1
ColabFold model
FPocket 0.268 · Pocket 2
P2Rank 0.888 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 303 / 4744 genomes with a hit
Normalized 0.064

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

8
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0043039 The chemical reactions and pathways by which the various amino acids become bonded to their corresponding tRNAs. The most common route for synthesis of aminoacyl tRNA is by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA and the alpha carboxylic acid group of an amino acid, usually catalyzed by the cognate aminoacyl-tRNA ligase. A given aminoacyl-tRNA ligase aminoacylates all species of an isoaccepting group of tRNA molecules.
  • GO:0004829 Catalysis of the reaction: ATP + L-threonine + tRNA(Thr) = AMP + diphosphate + L-threonyl-tRNA(Thr).
  • GO:0006435 The process of coupling threonine to threonyl-tRNA, catalyzed by threonyl-tRNA synthetase. The threonyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a threonine-accetping tRNA.
  • GO:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
  • 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:0006418 The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA and the alpha carboxylic acid group of an amino acid, to be used in ribosome-mediated polypeptide synthesis.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Sequence Features

Domain/signature hits from InterPro and related databases.

53 records
Show feature table
Start End DB Term Name
1 41 Pfam PF02824 TGS domain
1 41 InterPro IPR004095 TGS
48 202 Gene3D G3DSA:3.30.980.10 -
512 619 FunFam G3DSA:3.40.50.800:FF:000001 Threonine--tRNA ligase
46 614 Hamap MF_00184 Threonine--tRNA ligase [thrS].
46 614 InterPro IPR002320 Threonine-tRNA ligase, class IIa
223 514 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile.
223 514 InterPro IPR006195 Aminoacyl-tRNA synthetase, class II
1 44 Gene3D G3DSA:3.10.20.30 -
1 44 InterPro IPR012675 Beta-grasp domain superfamily
1 41 ProSiteProfiles PS51880 TGS domain profile.
52 611 NCBIfam TIGR00418 threonine--tRNA ligase
52 611 InterPro IPR002320 Threonine-tRNA ligase, class IIa
444 472 PRINTS PR01047 Threonyl-tRNA synthetase signature
444 472 InterPro IPR002320 Threonine-tRNA ligase, class IIa
309 337 PRINTS PR01047 Threonyl-tRNA synthetase signature
309 337 InterPro IPR002320 Threonine-tRNA ligase, class IIa
342 365 PRINTS PR01047 Threonyl-tRNA synthetase signature
342 365 InterPro IPR002320 Threonine-tRNA ligase, class IIa
487 500 PRINTS PR01047 Threonyl-tRNA synthetase signature
487 500 InterPro IPR002320 Threonine-tRNA ligase, class IIa
514 526 PRINTS PR01047 Threonyl-tRNA synthetase signature
514 526 InterPro IPR002320 Threonine-tRNA ligase, class IIa
510 616 SUPERFAMILY SSF52954 Class II aaRS ABD-related
2 615 PANTHER PTHR11451 THREONINE-TRNA LIGASE
110 167 FunFam G3DSA:3.30.54.20:FF:000002 Threonine--tRNA ligase
222 519 CDD cd00771 ThrRS_core
222 519 InterPro IPR033728 Threonine-tRNA ligase catalytic core domain
1 41 SUPERFAMILY SSF81271 TGS-like
1 41 InterPro IPR012676 TGS-like
45 203 FunFam G3DSA:3.30.980.10:FF:000005 Threonyl-tRNA synthetase, mitochondrial
90 110 Coils Coil Coil
205 512 FunFam G3DSA:3.30.930.10:FF:000002 Threonine--tRNA ligase
152 199 Pfam PF07973 Threonyl and Alanyl tRNA synthetase second additional domain
152 199 InterPro IPR012947 Threonyl/alanyl tRNA synthetase, SAD
298 508 Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T)
298 508 InterPro IPR002314 Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)
43 221 SUPERFAMILY SSF55186 ThrRS/AlaRS common domain
43 221 InterPro IPR018163 Threonyl/alanyl tRNA synthetase, class II-like, putative editing domain superfamily
519 609 CDD cd00860 ThrRS_anticodon
519 609 InterPro IPR047246 Threonine-tRNA ligase, class IIa, anticodon-binding domain
223 505 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases
223 505 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
512 622 Gene3D G3DSA:3.40.50.800 -
512 622 InterPro IPR036621 Anticodon-binding domain superfamily
150 199 SMART SM00863 tRNA_SAD_4
150 199 InterPro IPR012947 Threonyl/alanyl tRNA synthetase, SAD
521 610 Pfam PF03129 Anticodon binding domain
521 610 InterPro IPR004154 Anticodon-binding
203 511 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2
203 511 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
1 46 CDD cd01667 TGS_ThrRS
110 167 Gene3D G3DSA:3.30.54.20 -

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_A0A0H3GPK3
AlphaFold full sequence Viewing
ColabFold VK055_0276
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 0.204

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 15.24 0.75
2 5.95 0.292
3 3.41 0.122
4 1.34 0.015
5 1.33 0.015

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.

90 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
1B3 P0A8M3 435.9 Da LogP 1.05 TPSA 161.3 ✓ Ro5 ✓ Clean C[C@H]([C@@H](C(=O)NS(=O)(=O)c1cccc(c1)c2ccc3c(…
2CR P0A8M3 489.7 Da LogP 4.64 TPSA 127.9 ✓ Ro5 ✓ Clean CC1CC(CC(C(C(=CC=CCC(OC(=O)CC(C(C1)C)O)C2CCCC2C…
409 P0A8M3 401.4 Da LogP 0.39 TPSA 161.3 ✓ Ro5 ✓ Clean C[C@H]([C@@H](C(=O)NS(=O)(=O)c1cccc(c1)c2ccc3c(…
A3S P0A8M3 353.3 Da LogP -3.54 TPSA 194.7 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
BC9 P26639 477.6 Da LogP 4.47 TPSA 127.9 ✓ Ro5 ✓ Clean CC1CC(CC(C(C(=CCCCC(OC(=O)CC(C(C1)C)O)C2CCC2C(=…
E4O V7II86 385.3 Da LogP 1.08 TPSA 110.2 ✓ Ro5 ✓ Clean C[C@H]([C@@H](C(=O)NC/C=C/CN1C=Nc2cc(c(cc2C1=O)…
FQL V7II86 399.3 Da LogP 1.34 TPSA 96.2 ✓ Ro5 ✓ Clean C[C@H]([C@@H](C(=O)NC/C=C/CN1C=Nc2cc(c(cc2C1=O)…
FQR V7II86 430.7 Da LogP 1.62 TPSA 107.4 ✓ Ro5 ✓ Clean C[C@H]([C@@H](C(=O)OC/C=C/CN1C=Nc2cc(c(cc2C1=O)…
FQU V7II86 446.7 Da LogP 2.23 TPSA 107.4 ✓ Ro5 ✓ Clean C[C@H]([C@@H](C(=O)OCCCCCN1C=Nc2cc(c(cc2C1=O)Cl…
SSA P0A8M3 433.4 Da LogP -4.28 TPSA 238.0 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
TSB P0A8M3 447.4 Da LogP -3.89 TPSA 238.0 2 viol. ✓ Clean C[C@H]([C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@…
X16 P0A8M3 415.5 Da LogP 0.70 TPSA 161.3 ✓ Ro5 ✓ Clean Cc1nc2cc(ccc2c(n1)N)c3cccc(c3)S(=O)(=O)NC(=O)[C…

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.