Protein profile

VK055_0502

tyrosine--tRNA ligase

Genome: KpATCC43816

Gene: tyrS AIK79125.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GTN6
Amino acids 424
Annotations 10
Features 34
PDB binders 8
Druggability 0.419

Overview

Basic information about this protein and its source genome.

Accession
VK055_0502
Gene
tyrS AIK79125.1
Status
annotated
Amino acids
424
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
42.041
Human E-value
1.37e-53
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
95.519
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
95.11

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 0.419
Structure A0A0H3GTN6
Pocket Pocket 9
P2Rank 0.909
Structure A0A0H3GTN6
Pocket Pocket 1
ColabFold model
FPocket 0.495 · Pocket 15
P2Rank 0.933 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 238 / 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 9 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

9
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0006437 The process of coupling tyrosine to tyrosyl-tRNA, catalyzed by tyrosyl-tRNA synthetase. The tyrosyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a tyrosine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
  • GO:0004831 Catalysis of the reaction: L-tyrosine + ATP + tRNA(Tyr) = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + 2 H+.
  • GO:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
  • GO:0003723 Binding to an RNA molecule or a portion thereof.
  • 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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0042803 Binding to an identical protein to form a homodimer.

Sequence Features

Domain/signature hits from InterPro and related databases.

34 records
Show feature table
Start End DB Term Name
1 227 FunFam G3DSA:3.40.50.620:FF:000008 Tyrosine--tRNA ligase
327 423 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif
357 414 ProSiteProfiles PS50889 S4 RNA-binding domain profile.
4 328 SUPERFAMILY SSF52374 Nucleotidylyl transferase
1 227 Gene3D G3DSA:3.40.50.620 HUPs
1 227 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
358 419 SMART SM00363 s4_6
358 419 InterPro IPR002942 RNA-binding S4 domain
31 328 Pfam PF00579 tRNA synthetases class I (W and Y)
31 328 InterPro IPR002305 Aminoacyl-tRNA synthetase, class Ic
4 423 Hamap MF_02006 Tyrosine--tRNA ligase [tyrS].
4 423 InterPro IPR024107 Tyrosine-tRNA ligase, bacterial-type, type 1
333 424 FunFam G3DSA:3.10.290.10:FF:000007 Tyrosine--tRNA ligase
34 310 CDD cd00805 TyrRS_core
34 310 InterPro IPR002307 Tyrosine-tRNA ligase
359 404 CDD cd00165 S4
228 330 FunFam G3DSA:1.10.240.10:FF:000001 Tyrosine--tRNA ligase
228 332 Gene3D G3DSA:1.10.240.10 -
333 424 Gene3D G3DSA:3.10.290.10 -
333 424 InterPro IPR036986 RNA-binding S4 domain superfamily
46 68 PRINTS PR01040 Tyrosyl-tRNA synthetase signature
46 68 InterPro IPR002307 Tyrosine-tRNA ligase
188 210 PRINTS PR01040 Tyrosyl-tRNA synthetase signature
188 210 InterPro IPR002307 Tyrosine-tRNA ligase
167 182 PRINTS PR01040 Tyrosyl-tRNA synthetase signature
167 182 InterPro IPR002307 Tyrosine-tRNA ligase
221 233 PRINTS PR01040 Tyrosyl-tRNA synthetase signature
221 233 InterPro IPR002307 Tyrosine-tRNA ligase
2 424 NCBIfam TIGR00234 tyrosine--tRNA ligase
2 424 InterPro IPR002307 Tyrosine-tRNA ligase
42 52 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature.
42 52 InterPro IPR001412 Aminoacyl-tRNA synthetase, class I, conserved site
3 423 PANTHER PTHR11766 TYROSYL-TRNA SYNTHETASE
3 423 InterPro IPR024088 Tyrosine-tRNA ligase, bacterial-type

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_A0A0H3GTN6
AlphaFold full sequence Viewing
ColabFold VK055_0502
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
7 0.053
1 0.003
29 0.003
4 0.002

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 31.33 0.909
2 7.17 0.312
3 2.7 0.065
4 1.81 0.028
5 1.76 0.027

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.

65 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
AZY P0AGJ9 222.2 Da LogP 1.29 TPSA 132.3 ✓ Ro5 Alert c1cc(c(cc1C[C@@H](C(=O)O)N)N=[N+]=[N-])O
IYR P0AGJ9 307.1 Da LogP 0.95 TPSA 83.5 ✓ Ro5 ✓ Clean c1cc(c(cc1C[C@@H](C(=O)O)N)I)O
TYE P83453 167.2 Da LogP 0.25 TPSA 66.5 ✓ Ro5 ✓ Clean c1cc(ccc1C[C@@H](CO)N)O
TYS P0AGJ9 261.3 Da LogP -0.18 TPSA 126.9 ✓ Ro5 ✓ Clean c1cc(ccc1C[C@@H](C(=O)O)N)OS(=O)(=O)O
Y3U P0AGJ9 500.5 Da LogP -3.18 TPSA 212.4 2 viol. ✓ Clean CN1C(=O)C=CN(C1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)…
YSA P0AGJ9 509.5 Da LogP -2.32 TPSA 238.0 3 viol. ✓ Clean c1cc(ccc1C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]2[C@H](…
YSC P0AGJ9 485.5 Da LogP -2.90 TPSA 229.3 2 viol. ✓ Clean c1cc(ccc1C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]2[C@H](…
YSU P0AGJ9 486.5 Da LogP -3.19 TPSA 223.3 2 viol. ✓ Clean c1cc(ccc1C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]2[C@H](…

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.