Protein profile

KP13_01784

Prolyl-tRNA synthetase

Genome: KpKP13

Gene: proS AHE46224.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GS78
Amino acids 572
Annotations 10
Features 45
PDB binders 10
Druggability 0.725

Overview

Basic information about this protein and its source genome.

Accession
KP13_01784
Gene
proS AHE46224.1
Status
annotated
Amino acids
572
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
45.575
Human E-value
6.860000000000001e-64
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
94.755
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
95.43

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 0.725
Structure A0A0H3GS78
Pocket Pocket 1
P2Rank 0.924
Structure A0A0H3GS78
Pocket Pocket 1
ColabFold model
FPocket 0.415 · Pocket 20
P2Rank 0.876 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 405 / 4744 genomes with a hit
Normalized 0.085

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:0004827 Catalysis of the reaction: ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro).
  • GO:0002161 The hydrolysis of an incorrectly aminoacylated tRNA.
  • GO:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • 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: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:0006433 The process of coupling proline to prolyl-tRNA, catalyzed by prolyl-tRNA synthetase. The prolyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a methionine-accetping tRNA.
  • 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.

45 records
Show feature table
Start End DB Term Name
95 459 Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T)
95 459 InterPro IPR002314 Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)
388 467 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2
388 467 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
1 572 PIRSF PIRSF001535 ProRS_1
1 572 InterPro IPR023717 Prolyl-tRNA synthetase, class IIa, type 1
1 571 Hamap MF_01569 Proline--tRNA ligase [proS].
1 571 InterPro IPR023717 Prolyl-tRNA synthetase, class IIa, type 1
242 387 Gene3D G3DSA:3.90.960.10 -
242 387 InterPro IPR036754 YbaK/aminoacyl-tRNA synthetase-associated domain superfamily
219 390 SUPERFAMILY SSF55826 YbaK/ProRS associated domain
219 390 InterPro IPR036754 YbaK/aminoacyl-tRNA synthetase-associated domain superfamily
342 460 FunFam G3DSA:3.30.930.10:FF:000097 Proline--tRNA ligase
1 568 NCBIfam TIGR00409 proline--tRNA ligase
1 568 InterPro IPR004500 Prolyl-tRNA synthetase, class IIa, bacterial-type
473 567 CDD cd00861 ProRS_anticodon_short
473 567 InterPro IPR044140 Proline--tRNA ligase, anticodon binding domain
226 387 CDD cd04334 ProRS-INS
2 568 PANTHER PTHR42753 MITOCHONDRIAL RIBOSOME PROTEIN L39/PROLYL-TRNA LIGASE FAMILY MEMBER
10 478 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases
10 478 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
3 241 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2
3 241 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
257 376 Pfam PF04073 Aminoacyl-tRNA editing domain
257 376 InterPro IPR007214 YbaK/aminoacyl-tRNA synthetase-associated domain
134 142 PRINTS PR01046 Prolyl-tRNA synthetase signature
134 142 InterPro IPR002316 Proline-tRNA ligase, class IIa
68 86 PRINTS PR01046 Prolyl-tRNA synthetase signature
68 86 InterPro IPR002316 Proline-tRNA ligase, class IIa
144 155 PRINTS PR01046 Prolyl-tRNA synthetase signature
144 155 InterPro IPR002316 Proline-tRNA ligase, class IIa
104 115 PRINTS PR01046 Prolyl-tRNA synthetase signature
104 115 InterPro IPR002316 Proline-tRNA ligase, class IIa
244 386 FunFam G3DSA:3.90.960.10:FF:000001 Proline--tRNA ligase
468 566 Gene3D G3DSA:3.40.50.800 -
468 566 InterPro IPR036621 Anticodon-binding domain superfamily
38 468 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile.
38 468 InterPro IPR006195 Aminoacyl-tRNA synthetase, class II
15 303 FunFam G3DSA:3.30.930.10:FF:000043 Proline--tRNA ligase
462 571 SUPERFAMILY SSF52954 Class II aaRS ABD-related
475 567 Pfam PF03129 Anticodon binding domain
475 567 InterPro IPR004154 Anticodon-binding
17 458 CDD cd00779 ProRS_core_prok
17 458 InterPro IPR033730 Prokaryote proline-tRNA ligase core domain
468 566 FunFam G3DSA:3.40.50.800:FF:000006 Proline--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_A0A0H3GS78
AlphaFold full sequence Viewing
ColabFold KP13_01784
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 0.725
2 0.548

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 18.9 0.832
2 6.13 0.305
3 1.43 0.019
4 1.34 0.015

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.

81 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
5CA O26708 449.5 Da LogP -3.34 TPSA 217.8 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
86U S8G8I1 321.3 Da LogP 1.78 TPSA 64.0 ✓ Ro5 ✓ Clean c1c2c(cc(c1F)F)N=CN(C2=O)CCC[C@@H]3C(=O)CCCN3
86X S8G8I1 337.8 Da LogP 2.29 TPSA 64.0 ✓ Ro5 ✓ Clean c1c2c(cc(c1Cl)F)N=CN(C2=O)CCC[C@@H]3C(=O)CCCN3
873 S8G8I1 303.4 Da LogP 0.26 TPSA 87.4 ✓ Ro5 ✓ Clean c1ccc2c(c1)C(=O)N(C=N2)C[C@@H](C[C@@H]3[C@@H](C…
87C S8G8I1 305.4 Da LogP 0.19 TPSA 84.2 ✓ Ro5 ✓ Clean C1CCC2=C(C1)C(=O)N(C=N2)CC(=O)C[C@@H]3[C@@H](CC…
87F S8G8I1 285.3 Da LogP 1.50 TPSA 64.0 ✓ Ro5 ✓ Clean c1ccc2c(c1)C(=O)N(C=N2)CCC[C@@H]3C(=O)CCCN3
9SF S8G8I1 301.3 Da LogP 0.47 TPSA 84.2 ✓ Ro5 ✓ Clean c1ccc2c(c1)C(=O)N(C=N2)CC(=O)C[C@@H]3[C@H](CCCN…
A5A O26708 417.4 Da LogP -3.25 TPSA 217.8 1 viol. ✓ Clean C[C@@H](C(=O)NS(=O)(=O)OC[C@@H]1[C@H]([C@H]([C@…
ANP A0A4V8H034 506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
HFG A0A4V8H034 414.7 Da LogP 1.88 TPSA 84.2 ✓ Ro5 ✓ Clean c1c2c(cc(c1Cl)Br)N=CN(C2=O)CC(=O)C[C@@H]3[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.