Protein profile

KP13_04672

Phenylalanyl-tRNA synthetase beta chain

Genome: KpKP13

Gene: pheT AHE44068.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GUX6
Amino acids 795
Annotations 8
Features 53
PDB binders 4
Druggability 0.821

Overview

Basic information about this protein and its source genome.

Accession
KP13_04672
Gene
pheT AHE44068.1
Status
annotated
Amino acids
795
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
22.716
Human E-value
5.5e-10
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
92.453
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
95.58

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 0.821
Structure A0A0H3GUX6
Pocket Pocket 1
P2Rank 0.876
Structure A0A0H3GUX6
Pocket Pocket 1
ColabFold model
FPocket 0.566 · Pocket 2
P2Rank 0.799 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 153 / 4744 genomes with a hit
Normalized 0.032

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:0004826 Catalysis of the reaction: ATP + L-phenylalanine + tRNA(Phe) = AMP + diphosphate + L-phenylalanyl-tRNA(Phe).
  • GO:0000049 Binding to a transfer RNA.
  • GO:0006432 The process of coupling phenylalanine to phenylalanyl-tRNA, catalyzed by phenylalanyl-tRNA synthetase. The phenylalanyl-tRNA synthetase is a class-II synthetase. However, unlike other class II enzymes, The activated amino acid is transferred to the 2'-OH group of a phenylalanine-accepting tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • 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:0009328 An enzyme complex that catalyzes the ligation of phenylalanine to tRNA(Phe), forming L-phenylalanyl-tRNA(Phe).

Sequence Features

Domain/signature hits from InterPro and related databases.

53 records
Show feature table
Start End DB Term Name
45 145 Pfam PF01588 Putative tRNA binding domain
45 145 InterPro IPR002547 tRNA-binding domain
1 788 Hamap MF_00283 Phenylalanine--tRNA ligase beta subunit [pheT].
1 788 InterPro IPR004532 Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type
696 794 SUPERFAMILY SSF54991 Anticodon-binding domain of PheRS
696 794 InterPro IPR036690 Ferrodoxin-fold anticodon-binding domain superfamily
401 476 ProSiteProfiles PS51483 B5 domain profile.
401 476 InterPro IPR005147 tRNA synthetase, B5-domain
53 147 CDD cd02796 tRNA_bind_bactPheRS
53 147 InterPro IPR033714 Phenylalanly tRNA synthetase, tRNA-binding-domain
196 397 FunFam G3DSA:3.50.40.10:FF:000001 Phenylalanine--tRNA ligase beta subunit
475 685 Pfam PF17759 Phenylalanyl tRNA synthetase beta chain CLM domain
475 685 InterPro IPR041616 Phenylalanyl tRNA synthetase beta chain, core domain
404 475 SUPERFAMILY SSF46955 Putative DNA-binding domain
404 475 InterPro IPR009061 Putative DNA-binding domain superfamily
701 794 Pfam PF03147 Ferredoxin-fold anticodon binding domain
701 794 InterPro IPR005121 Ferrodoxin-fold anticodon-binding domain
403 471 SMART SM00874 B5_2
403 471 InterPro IPR005147 tRNA synthetase, B5-domain
212 385 SMART SM00873 B3_4_2
212 385 InterPro IPR005146 B3/B4 tRNA-binding domain
401 475 Gene3D G3DSA:3.30.56.10 -
702 795 Gene3D G3DSA:3.30.70.380 -
702 795 InterPro IPR036690 Ferrodoxin-fold anticodon-binding domain superfamily
485 693 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2
485 693 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
1 794 NCBIfam TIGR00472 phenylalanine--tRNA ligase subunit beta
1 794 InterPro IPR004532 Phenylalanine-tRNA ligase, class IIc, beta subunit, bacterial type
702 795 FunFam G3DSA:3.30.70.380:FF:000001 Phenylalanine--tRNA ligase beta subunit
4 686 PANTHER PTHR10947 PHENYLALANYL-TRNA SYNTHETASE BETA CHAIN AND LEUCINE-RICH REPEAT-CONTAINING PROTEIN 47
4 686 InterPro IPR045060 Phenylalanine-tRNA ligase, class IIc, beta subunit
487 692 FunFam G3DSA:3.30.930.10:FF:000022 Phenylalanine--tRNA ligase beta subunit
467 690 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases
467 690 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
39 148 ProSiteProfiles PS50886 tRNA-binding domain profile.
39 148 InterPro IPR002547 tRNA-binding domain
7 180 Gene3D G3DSA:3.30.56.10 -
39 154 Gene3D G3DSA:2.40.50.140 -
39 154 InterPro IPR012340 Nucleic acid-binding, OB-fold
197 395 Gene3D G3DSA:3.50.40.10 -
197 395 InterPro IPR020825 Phenylalanyl-tRNA synthetase-like, B3/B4
39 154 FunFam G3DSA:2.40.50.140:FF:000045 Phenylalanine--tRNA ligase beta subunit
35 197 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
35 197 InterPro IPR012340 Nucleic acid-binding, OB-fold
195 396 SUPERFAMILY SSF56037 PheT/TilS domain
701 794 SMART SM00896 FDX_ACB_2
402 475 FunFam G3DSA:3.30.56.10:FF:000002 Phenylalanine--tRNA ligase beta subunit
212 385 Pfam PF03483 B3/4 domain
406 471 Pfam PF03484 tRNA synthetase B5 domain
406 471 InterPro IPR005147 tRNA synthetase, B5-domain
701 794 ProSiteProfiles PS51447 Ferredoxin-fold anticodon binding (FDX-ACB) domain profile.
495 689 CDD cd00769 PheRS_beta_core
495 689 InterPro IPR041616 Phenylalanyl tRNA synthetase beta chain, core domain

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_A0A0H3GUX6
AlphaFold full sequence Viewing
ColabFold KP13_04672
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 0.821
3 0.475
32 0.232
6 0.227

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 13.84 0.701
2 7.84 0.416
3 2.77 0.084
4 2.6 0.075
5 1.95 0.041

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.

54 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
DAH P27002 197.2 Da LogP 0.05 TPSA 103.8 ✓ Ro5 Alert c1cc(c(cc1C[C@@H](C(=O)O)N)O)O
MTY Q5SGX1 181.2 Da LogP 0.35 TPSA 83.5 ✓ Ro5 ✓ Clean c1cc(cc(c1)O)C[C@@H](C(=O)O)N
PUY Q5SGX1 471.5 Da LogP -0.79 TPSA 160.9 1 viol. ✓ Clean CN(C)c1c2c(ncn1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H]…
TAM Q7MXR4 163.2 Da LogP -1.17 TPSA 86.7 ✓ Ro5 ✓ Clean C(CO)C(CCO)(CCO)N

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.