Protein profile

PA0956

proline--tRNA ligase

Genome: NC_002516.2

Gene: PA0956 proS Structure source: Experimental + AlphaFold UniProt Q9I502
Amino acids 571
Annotations 10
Features 45
PDB binders 5
Druggability 0.622

Overview

Basic information about this protein and its source genome.

Accession
PA0956
Gene
PA0956 proS
Status
annotated
Amino acids
571
Structure source
Experimental + AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
47.788
Human E-value
5.1000000000000005e-67
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 0.622
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MRTSQYLLSTLKETPADAVVISHQLLLRAGMIRRLASGLYTWLPMGLRVLRKVETIVREEMNAAGALEVLMPAVQPAELWQESGRWEQYGPELLRLKDRHEREFCVGPTHEEVITDLARNELNSYKQLPINFYQIQTKFRDEIRPRFGLMRGREFIMKDAYSFHLSQDSLQQTYDGMYQAYSKIFSRLGLDFRPVQADNGSIGGSGSHEFHVLANSGEDDIVFSDSSDYAANIEKAEAVPRESARGSATEDMRLVDTPNTKTIAALVDGFQLPIEKTIKTLVVHGAEEGTLVALIVRGDHELNEIKAANQPLVASPLVFASEAEIRAAIGAGPGSLGPVNLPIACIVDRSVALMSDFAAGANIEDKHYFGVNWERDLPLPEVADLRNVVEGDPSPDGKGTLVIKRGIEVGHIFQLGTKYSEAMKLSVLSEQGKPVNLIMGCYGIGVSRVVAAAIEQNHDERGILWPSALAPFQIALVPLKYETESVKQATDKLYAELTAAGFEVLLDDRDKKTSPGVKFADMELIGIPHRIVISDRGLSEGVLEYKGRRDSESQNLPIGELMSFITEKLSR

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:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0002161 The hydrolysis of an incorrectly aminoacylated tRNA.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0004827 Catalysis of the reaction: ATP + L-proline + tRNA(Pro) = AMP + diphosphate + L-prolyl-tRNA(Pro).
  • 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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • 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.

45 records
Show feature table
Start End DB Term Name
33 466 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile.
33 466 InterPro IPR006195 Aminoacyl-tRNA synthetase, class II
3 242 FunFam G3DSA:3.30.930.10:FF:000012 Proline--tRNA ligase
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
104 115 PRINTS PR01046 Prolyl-tRNA synthetase signature
104 115 InterPro IPR002316 Proline-tRNA ligase, class IIa
144 155 PRINTS PR01046 Prolyl-tRNA synthetase signature
144 155 InterPro IPR002316 Proline-tRNA ligase, class IIa
3 243 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2
3 243 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
244 384 Gene3D G3DSA:3.90.960.10 -
244 384 InterPro IPR036754 YbaK/aminoacyl-tRNA synthetase-associated domain superfamily
95 457 Pfam PF00587 tRNA synthetase class II core domain (G, H, P, S and T)
95 457 InterPro IPR002314 Aminoacyl-tRNA synthetase, class II (G/ P/ S/T)
226 385 CDD cd04334 ProRS-INS
466 565 FunFam G3DSA:3.40.50.800:FF:000006 Proline--tRNA ligase
2 566 PANTHER PTHR42753 MITOCHONDRIAL RIBOSOME PROTEIN L39/PROLYL-TRNA LIGASE FAMILY MEMBER
466 565 Gene3D G3DSA:3.40.50.800 -
466 565 InterPro IPR036621 Anticodon-binding domain superfamily
461 570 SUPERFAMILY SSF52954 Class II aaRS ABD-related
471 566 CDD cd00861 ProRS_anticodon_short
471 566 InterPro IPR044140 Proline--tRNA ligase, anticodon binding domain
340 458 FunFam G3DSA:3.30.930.10:FF:000097 Proline--tRNA ligase
10 476 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases
10 476 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
385 465 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2
385 465 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
244 384 FunFam G3DSA:3.90.960.10:FF:000001 Proline--tRNA ligase
1 571 PIRSF PIRSF001535 ProRS_1
1 571 InterPro IPR023717 Prolyl-tRNA synthetase, class IIa, type 1
1 567 NCBIfam TIGR00409 proline--tRNA ligase
1 567 InterPro IPR004500 Prolyl-tRNA synthetase, class IIa, bacterial-type
17 456 CDD cd00779 ProRS_core_prok
17 456 InterPro IPR033730 Prokaryote proline-tRNA ligase core domain
473 567 Pfam PF03129 Anticodon binding domain
473 567 InterPro IPR004154 Anticodon-binding
218 388 SUPERFAMILY SSF55826 YbaK/ProRS associated domain
218 388 InterPro IPR036754 YbaK/aminoacyl-tRNA synthetase-associated domain superfamily
1 570 Hamap MF_01569 Proline--tRNA ligase [proS].
1 570 InterPro IPR023717 Prolyl-tRNA synthetase, class IIa, type 1
257 375 Pfam PF04073 Aminoacyl-tRNA editing domain
257 375 InterPro IPR007214 YbaK/aminoacyl-tRNA synthetase-associated 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

4 + 1

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

Entry Method Resolution Chain Coverage Links Status
PDB 8W8J
X-ray 1.81 Å A,B
100.0% 1-571
Viewing
PDB 8W8L
X-ray 1.82 Å A,B
100.0% 1-571
Loaded
PDB 8W9I
X-ray 2.45 Å A,B
100.0% 1-571
Loaded
PDB 5UCM
X-ray 2.60 Å A,B
100.0% 1-571
Loaded
AlphaFold PA0956
AlphaFold 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 0.622
1 0.208

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 21.99 0.876
2 2.57 0.073
3 2.22 0.054
4 2.04 0.045
5 1.28 0.013

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.

75 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 Q6N5P6 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)…
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](…
P5A Q6N5P6 443.4 Da LogP -2.84 TPSA 203.8 1 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…

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.