Protein profile

PA4439

tryptophan--tRNA ligase

Genome: NC_002516.2

Gene: PA4439 trpS Structure source: AlphaFold UniProt Q9HVX6
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Amino acids 448
Annotations 8
Features 28
PDB binders 7
Druggability 0.65

Overview

Basic information about this protein and its source genome.

Accession
PA4439
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA4439 trpS
Status
annotated
Amino acids
448
Structure source
AlphaFold
EC
6.1.1.2
GO
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0004830 Catalysis of the reaction: ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + L-tryptophanyl-tRNA(Trp). GO:0006436 The process of coupling tryptophan to tryptophanyl-tRNA, catalyzed by tryptophanyl-tRNA synthetase. The tryptophanyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a tryptophan-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification. 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:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
29.882
Human E-value
2.54e-41
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected Druggability evidence

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 0.65
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

MTTRILTGITPTGTPHLGNYAGAIRPAILASRRSDVDSFYFLADYHALIKCDDPARIQRSRLEIAATWLAGGLDVERATFYRQSDIPEIPELTWLLTCVSAKGLLNRAHAYKAAVDRNVEAGEDPDAGVTMGLYSYPVLMAADILMFNAHKIPVGRDQVQHVEMARDIGQRFNHLFGNGREFFVLPEAVIEENVATLPGLDGRKMSKSYDNTIPLFSPSRQLKDAIARIVTDSRAPGEPKDPDSSHLFLLYSAFASAEQVAAFRQELLEGLAWGEAKQRLFQLLDNELGEARERYQALIAKPDDIEDILLAGAAKARRIATPFIAELREAVGLRSLREPLKSAESGKKKAAKAARLVSFRDDDGSFRFRLLDAAGEQLLLSRAFADGKAAGAVSKRLLAGETADLRAEGNAFGLWLDGEAVAQSPAFADAAARDAAIERTREALAPQE

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0004830 Catalysis of the reaction: ATP + L-tryptophan + tRNA(Trp) = AMP + diphosphate + L-tryptophanyl-tRNA(Trp).
  • GO:0006436 The process of coupling tryptophan to tryptophanyl-tRNA, catalyzed by tryptophanyl-tRNA synthetase. The tryptophanyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a tryptophan-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
  • 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:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

28 records
Show feature table
Start End DB Term Name
356 398 SUPERFAMILY SSF160113 YegP-like
356 398 InterPro IPR036913 YegP-like superfamily
199 301 FunFam G3DSA:1.10.240.10:FF:000005 Tryptophan--tRNA ligase
11 20 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature.
11 20 InterPro IPR001412 Aminoacyl-tRNA synthetase, class I, conserved site
3 243 Pfam PF00579 tRNA synthetases class I (W and Y)
3 243 InterPro IPR002305 Aminoacyl-tRNA synthetase, class Ic
281 301 Coils Coil Coil
5 203 FunFam G3DSA:3.40.50.620:FF:000144 Tryptophan--tRNA ligase
2 334 Hamap MF_00140_B Tryptophan--tRNA ligase [trpS].
2 334 InterPro IPR024109 Tryptophan-tRNA ligase, bacterial-type
150 171 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature
150 171 InterPro IPR002306 Tryptophan-tRNA ligase
67 86 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature
67 86 InterPro IPR002306 Tryptophan-tRNA ligase
15 31 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature
15 31 InterPro IPR002306 Tryptophan-tRNA ligase
204 214 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature
204 214 InterPro IPR002306 Tryptophan-tRNA ligase
3 333 PANTHER PTHR43766 TRYPTOPHAN--TRNA LIGASE, MITOCHONDRIAL
4 287 CDD cd00806 TrpRS_core
4 287 InterPro IPR002306 Tryptophan-tRNA ligase
1 333 NCBIfam TIGR00233 tryptophan--tRNA ligase
1 333 InterPro IPR002306 Tryptophan-tRNA ligase
5 320 Gene3D G3DSA:3.40.50.620 HUPs
5 320 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
4 333 SUPERFAMILY SSF52374 Nucleotidylyl transferase
199 301 Gene3D G3DSA:1.10.240.10 -

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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Structural evidence

0 + 1

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA4439
AlphaFold — — full sequence — Viewing
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
1 0.65
4 0.247

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.

57 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
5BX
5DK4
P00953 257.3 Da LogP 1.77 TPSA 66.5 ✓ Ro5 ✓ Clean C[C@H](c1c[nH]c2c1cccc2)[C@H]3C(=O)N=C(O3)NC
9E0
7CMS
P00953 233.3 Da LogP 2.83 TPSA 53.1 ✓ Ro5 ✓ Clean C[C@H]1c2c[nH]c3c2c(ccc3)S[C@H]1C(=O)O
ANL
2OV4
P00953 93.1 Da LogP 1.27 TPSA 26.0 ✓ Ro5 ✓ Clean c1ccc(cc1)N
AQP
2OV4
P00953 587.2 Da LogP -1.51 TPSA 325.7 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
LTN
1MAU
P00953 203.2 Da LogP 0.52 TPSA 84.9 ✓ Ro5 ✓ Clean c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)N)N
NH4
1I6K
P00953 18.0 Da LogP 0.38 TPSA 36.5 ✓ Ro5 ✓ Clean [NH4+]
TYM
1I6K
P00953 533.4 Da LogP -0.26 TPSA 233.9 3 viol. ✓ Clean c1ccc2c(c1)c(c[nH]2)C[C@@H](C(=O)O[P@](=O)(O)OC…

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.