Protein profile

KP13_13547

Tryptophanyl-tRNA synthetase

Genome: KpKP13

Gene: ANJ86633.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GR40
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Amino acids 335
Annotations 8
Features 23
PDB binders 7
Druggability 0.265

Overview

Basic information about this protein and its source genome.

Accession
KP13_13547
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
ANJ86633.1
Status
annotated
Amino acids
335
Structure source
AlphaFold + ColabFold
EC
6.1.1.2
GO
GO:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP. 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: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: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: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.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
27.596
Human E-value
3.93e-26
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
63.692
DEG E-value
6.56e-157
Localization
Cytoplasmic
ColabFold pLDDT
94.76

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 0.265
Structure A0A0H3GR40
Pocket Pocket 1
P2Rank 0.894
Structure A0A0H3GR40
Pocket Pocket 1
ColabFold model
FPocket 0.316 · Pocket 21
P2Rank 0.884 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 1234 / 4744 genomes with a hit
Normalized 0.26

Sequence

Primary amino-acid sequence viewer.

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:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
  • 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: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: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: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.

Sequence Features

Domain/signature hits from InterPro and related databases.

23 records
Show feature table
Start End DB Term Name
6 285 CDD cd00806 TrpRS_core
6 285 InterPro IPR002306 Tryptophan-tRNA ligase
13 22 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature.
13 22 InterPro IPR001412 Aminoacyl-tRNA synthetase, class I, conserved site
192 299 FunFam G3DSA:1.10.240.10:FF:000005 Tryptophan--tRNA ligase
4 331 SUPERFAMILY SSF52374 Nucleotidylyl transferase
7 330 Gene3D G3DSA:3.40.50.620 HUPs
7 330 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
4 331 NCBIfam TIGR00233 tryptophan--tRNA ligase
4 331 InterPro IPR002306 Tryptophan-tRNA ligase
190 299 Gene3D G3DSA:1.10.240.10 -
7 221 FunFam G3DSA:3.40.50.620:FF:000094 Tryptophan--tRNA ligase
3 286 Pfam PF00579 tRNA synthetases class I (W and Y)
3 286 InterPro IPR002305 Aminoacyl-tRNA synthetase, class Ic
3 331 PANTHER PTHR43766 TRYPTOPHAN--TRNA LIGASE, MITOCHONDRIAL
68 87 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature
68 87 InterPro IPR002306 Tryptophan-tRNA ligase
146 167 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature
146 167 InterPro IPR002306 Tryptophan-tRNA ligase
198 208 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature
198 208 InterPro IPR002306 Tryptophan-tRNA ligase
17 33 PRINTS PR01039 Tryptophanyl-tRNA synthetase signature
17 33 InterPro IPR002306 Tryptophan-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

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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_A0A0H3GR40
AlphaFold — — full sequence — Viewing
ColabFold KP13_13547
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
1 0.265
5 0.231

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 7.54 0.397
2 2.77 0.084
3 2.16 0.051
4 1.8 0.034
5 1.21 0.011

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.