Protein profile

PA3834

valine--tRNA ligase

Genome: NC_002516.2

Gene: valS PA3834 Structure source: Experimental + AlphaFold UniProt Q9HXH0
Amino acids 950
Annotations 10
Features 52
PDB binders 2
Druggability 0.648

Overview

Basic information about this protein and its source genome.

Accession
PA3834
Gene
valS PA3834
Status
annotated
Amino acids
950
Structure source
Experimental + AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
52.885
Human E-value
1.95e-65
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 0.648
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

MDKTYQPHAIETSWYETWESNDYFAPSGEGQPYTIMIPPPNVTGSLHMGHGFNNAIMDALIRYRRMQGRNTLWQPGTDHAGIATQMVVERQLGAQGVSRHDLGREKFLEKVWEWKEQSGGNITRQIRRLGSSVDWSRERFTMDDGLSEAVKEAFVRLHEDGLIYRGKRLVNWDTKLHTAISDLEVENHDEKGHLWHLRYPLVNGAKTSEGLDYLVVATTRPETLLGDAAVAVHPEDERYAKLIGQFAELPIVGRHIPIIADEYVDREFGTGCVKITPAHDFNDYEVGKRHDLPLINIFDKNAAVLAQAQVFHLDGSVNPNLDPSLPQSYAGMDRFAARKAIVAEFEAMGLLEKVDDHALKVPKGDRSGTVIEPWLTDQWYVSTKPLAEDAIAAVEDGRIQFVPKQYENMYFSWMRDIQDWCISRQLWWGHRIPAWYDEAGNVYVGRDEVEVRTKHKLGNEAELRQDEDVLDTWFSSGLWTFSTLGWPQQTEFLKTFHPTDVLVTGFDIIFFWVARMIMLTMHLVKNPDGTPQIPFKTVYVHGLVRDGQGQKMSKSKGNVLDPLDIVDGIDLDTLLQKRTSGMMQPKLAEKIAKQTRAEFPEGIASYGTDALRFTFCSLASTGRDIKFDMGRVEGFRNFCNKIWNAANFVIENTDGQDTGVNGEPVELSSVDRWIISQLQRTEQEVTRQLDAFRFDLAAQALYEFIWDEYCAWYLELVKPVLWDENAPIERQRGTRRTLIRVLETALRLAHPFMPFITEEIWQRIKGQAGKEGPTLMLQPWPVADEGRIDAAAEGDIEWVKALMLGVRQIRGEMNISMAKRIDIILKNASPSDHRRLADNEPLLMKLAKLESIRVLEAGEEAPMSATALVGDMEVLVPMAGLIDKSAELGRLDKEIQRLEGEVKRVGGKLSNEGFVAKAPADVIEKERAKLAEAEQALAKLAEQRQKIAAL

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:0004832 Catalysis of the reaction: L-valine + ATP + tRNA(Val) = L-valyl-tRNA(Val) + AMP + diphosphate + 2 H+.
  • GO:0006438 The process of coupling valine to valyl-tRNA, catalyzed by valyl-tRNA synthetase. The valyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a valine-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
  • 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.

52 records
Show feature table
Start End DB Term Name
328 552 FunFam G3DSA:3.40.50.620:FF:000146 Valine--tRNA ligase
881 908 Coils Coil Coil
14 628 Pfam PF00133 tRNA synthetases class I (I, L, M and V)
14 628 InterPro IPR002300 Aminoacyl-tRNA synthetase, class Ia
3 202 Gene3D G3DSA:3.40.50.620 HUPs
3 202 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
876 947 Gene3D G3DSA:1.10.287.380 -
876 947 InterPro IPR037118 Valyl-tRNA synthetase, tRNA-binding arm superfamily
876 947 FunFam G3DSA:1.10.287.380:FF:000001 Valine--tRNA ligase
627 764 CDD cd07962 Anticodon_Ia_Val
627 764 InterPro IPR033705 Valyl tRNA synthetase, anticodon-binding domain
327 552 Gene3D G3DSA:3.40.50.620 HUPs
327 552 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
576 816 Gene3D G3DSA:1.10.730.10 -
240 310 Gene3D G3DSA:3.90.740.10 -
240 310 InterPro IPR009008 Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain
188 362 SUPERFAMILY SSF50677 ValRS/IleRS/LeuRS editing domain
188 362 InterPro IPR009008 Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain
203 239 Gene3D G3DSA:3.90.740.10 -
203 239 InterPro IPR009008 Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain
1 930 NCBIfam TIGR00422 valine--tRNA ligase
1 930 InterPro IPR002303 Valine-tRNA ligase
575 816 FunFam G3DSA:1.10.730.10:FF:000007 Valine--tRNA ligase
1 638 SUPERFAMILY SSF52374 Nucleotidylyl transferase
883 947 SUPERFAMILY SSF46589 tRNA-binding arm
883 947 InterPro IPR010978 Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm
3 198 FunFam G3DSA:3.40.50.620:FF:000020 Valine--tRNA ligase, mitochondrial
639 898 SUPERFAMILY SSF47323 Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
639 898 InterPro IPR009080 Aminoacyl-tRNA synthetase, class Ia, anticodon-binding
1 948 Hamap MF_02004 Valine--tRNA ligase [valS].
1 948 InterPro IPR002303 Valine-tRNA ligase
40 51 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature.
40 51 InterPro IPR001412 Aminoacyl-tRNA synthetase, class I, conserved site
1 945 PANTHER PTHR11946 VALYL-TRNA SYNTHETASES
1 945 InterPro IPR002303 Valine-tRNA ligase
923 950 Coils Coil Coil
886 947 Pfam PF10458 Valyl tRNA synthetase tRNA binding arm
886 947 InterPro IPR019499 Valyl-tRNA synthetase, tRNA-binding arm
671 823 Pfam PF08264 Anticodon-binding domain of tRNA ligase
671 823 InterPro IPR013155 Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding
233 250 PRINTS PR00986 Valyl-tRNA synthetase signature
233 250 InterPro IPR002303 Valine-tRNA ligase
466 487 PRINTS PR00986 Valyl-tRNA synthetase signature
466 487 InterPro IPR002303 Valine-tRNA ligase
366 379 PRINTS PR00986 Valyl-tRNA synthetase signature
366 379 InterPro IPR002303 Valine-tRNA ligase
497 515 PRINTS PR00986 Valyl-tRNA synthetase signature
497 515 InterPro IPR002303 Valine-tRNA ligase
33 44 PRINTS PR00986 Valyl-tRNA synthetase signature
33 44 InterPro IPR002303 Valine-tRNA ligase
32 627 CDD cd00817 ValRS_core
198 238 FunFam G3DSA:3.90.740.10:FF:000003 Valine--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

Loading 3D structure...

Legend High Medium Low

Structural evidence

1 + 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 4XKZ
X-ray 1.95 Å A
27.4% 639-898
Viewing
AlphaFold PA3834
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
3 0.648

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 4.91 0.221
2 2.42 0.065

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.

83 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
ILA P56690 458.5 Da LogP -2.65 TPSA 220.6 2 viol. ✓ Clean CC[C@H](C)[C@@H](C(=O)NS(=O)(=O)NC[C@@H]1[C@H](…
VAA P96142 444.5 Da LogP -3.04 TPSA 220.6 2 viol. ✓ Clean CC(C)[C@@H](C(=O)NS(=O)(=O)NC[C@@H]1[C@H]([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.