Protein profile

KP13_05164

Tyrosyl-tRNA synthetase

Genome: KpKP13

Gene: tyrS AHE44283.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GTN6
Amino acids 428
Annotations 10
Features 34
PDB binders 8
Druggability 0.419

Overview

Basic information about this protein and its source genome.

Accession
KP13_05164
Gene
tyrS AHE44283.1
Status
annotated
Amino acids
428
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
42.041
Human E-value
1.38e-53
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
95.519
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
94.45

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 0.491 · Pocket 18
P2Rank 0.925 · 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:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
  • GO:0004831 Catalysis of the reaction: L-tyrosine + ATP + tRNA(Tyr) = L-tyrosyl-tRNA(Tyr) + AMP + diphosphate + 2 H+.
  • 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: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:0003723 Binding to an RNA molecule or a portion thereof.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • 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: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
331 427 SUPERFAMILY SSF55174 Alpha-L RNA-binding motif
192 214 PRINTS PR01040 Tyrosyl-tRNA synthetase signature
192 214 InterPro IPR002307 Tyrosine-tRNA ligase
50 72 PRINTS PR01040 Tyrosyl-tRNA synthetase signature
50 72 InterPro IPR002307 Tyrosine-tRNA ligase
171 186 PRINTS PR01040 Tyrosyl-tRNA synthetase signature
171 186 InterPro IPR002307 Tyrosine-tRNA ligase
225 237 PRINTS PR01040 Tyrosyl-tRNA synthetase signature
225 237 InterPro IPR002307 Tyrosine-tRNA ligase
35 332 Pfam PF00579 tRNA synthetases class I (W and Y)
35 332 InterPro IPR002305 Aminoacyl-tRNA synthetase, class Ic
337 428 FunFam G3DSA:3.10.290.10:FF:000007 Tyrosine--tRNA ligase
5 231 Gene3D G3DSA:3.40.50.620 HUPs
5 231 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
337 428 Gene3D G3DSA:3.10.290.10 -
337 428 InterPro IPR036986 RNA-binding S4 domain superfamily
8 427 Hamap MF_02006 Tyrosine--tRNA ligase [tyrS].
8 427 InterPro IPR024107 Tyrosine-tRNA ligase, bacterial-type, type 1
38 314 CDD cd00805 TyrRS_core
38 314 InterPro IPR002307 Tyrosine-tRNA ligase
232 336 Gene3D G3DSA:1.10.240.10 -
363 408 CDD cd00165 S4
361 418 ProSiteProfiles PS50889 S4 RNA-binding domain profile.
362 423 SMART SM00363 s4_6
362 423 InterPro IPR002942 RNA-binding S4 domain
46 56 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature.
46 56 InterPro IPR001412 Aminoacyl-tRNA synthetase, class I, conserved site
6 427 PANTHER PTHR11766 TYROSYL-TRNA SYNTHETASE
6 427 InterPro IPR024088 Tyrosine-tRNA ligase, bacterial-type
5 231 FunFam G3DSA:3.40.50.620:FF:000008 Tyrosine--tRNA ligase
8 332 SUPERFAMILY SSF52374 Nucleotidylyl transferase
232 334 FunFam G3DSA:1.10.240.10:FF:000001 Tyrosine--tRNA ligase
6 428 NCBIfam TIGR00234 tyrosine--tRNA ligase
6 428 InterPro IPR002307 Tyrosine-tRNA ligase

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...

Legend High Medium Low

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 KP13_05164
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
9 0.419

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 17.87 0.81
2 7.48 0.393
3 2.42 0.065
4 1.77 0.032
5 1.06 0.007

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.