Protein profile

KP13_01303

Valyl-tRNA synthetase

Genome: KpKP13

Gene: AHE46631.1 valS Structure source: AlphaFold + ColabFold UniProt A0A0H3GQW8
Amino acids 951
Annotations 10
Features 55
PDB binders 3
Druggability 0.226

Overview

Basic information about this protein and its source genome.

Accession
KP13_01303
Gene
AHE46631.1 valS
Status
annotated
Amino acids
951
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
50.0
Human E-value
4.33e-63
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
96.109
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
93.31

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 0.226
Structure A0A0H3GQW8
Pocket Pocket 18
P2Rank 0.934
Structure A0A0H3GQW8
Pocket Pocket 1
ColabFold model
FPocket 0.289 · Pocket 14
P2Rank 0.941 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 222 / 4744 genomes with a hit
Normalized 0.047

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:0002161 The hydrolysis of an incorrectly aminoacylated tRNA.
  • 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: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:0004832 Catalysis of the reaction: L-valine + ATP + tRNA(Val) = L-valyl-tRNA(Val) + AMP + diphosphate + 2 H+.
  • 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: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.

55 records
Show feature table
Start End DB Term Name
331 555 FunFam G3DSA:3.40.50.620:FF:000146 Valine--tRNA ligase
344 555 Gene3D G3DSA:3.40.50.620 HUPs
344 555 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
1 949 Hamap MF_02004 Valine--tRNA ligase [valS].
1 949 InterPro IPR002303 Valine-tRNA ligase
579 817 Gene3D G3DSA:1.10.730.10 -
642 899 SUPERFAMILY SSF47323 Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
642 899 InterPro IPR009080 Aminoacyl-tRNA synthetase, class Ia, anticodon-binding
924 944 Coils Coil Coil
886 944 Pfam PF10458 Valyl tRNA synthetase tRNA binding arm
886 944 InterPro IPR019499 Valyl-tRNA synthetase, tRNA-binding arm
578 817 FunFam G3DSA:1.10.730.10:FF:000007 Valine--tRNA ligase
877 948 FunFam G3DSA:1.10.287.380:FF:000001 Valine--tRNA ligase
882 909 Coils Coil Coil
877 948 Gene3D G3DSA:1.10.287.380 -
877 948 InterPro IPR037118 Valyl-tRNA synthetase, tRNA-binding arm superfamily
191 365 SUPERFAMILY SSF50677 ValRS/IleRS/LeuRS editing domain
191 365 InterPro IPR009008 Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain
1 498 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
42 53 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature.
42 53 InterPro IPR001412 Aminoacyl-tRNA synthetase, class I, conserved site
2 200 Gene3D G3DSA:3.40.50.620 HUPs
2 200 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
674 824 Pfam PF08264 Anticodon-binding domain of tRNA ligase
674 824 InterPro IPR013155 Methionyl/Valyl/Leucyl/Isoleucyl-tRNA synthetase, anticodon-binding
33 630 CDD cd00817 ValRS_core
1 940 PANTHER PTHR11946 VALYL-TRNA SYNTHETASES
1 940 InterPro IPR002303 Valine-tRNA ligase
14 631 Pfam PF00133 tRNA synthetases class I (I, L, M and V)
14 631 InterPro IPR002300 Aminoacyl-tRNA synthetase, class Ia
1 641 SUPERFAMILY SSF52374 Nucleotidylyl transferase
884 947 SUPERFAMILY SSF46589 tRNA-binding arm
884 947 InterPro IPR010978 Class I and II aminoacyl-tRNA synthetase, tRNA-binding arm
499 517 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane.
518 951 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm.
630 764 CDD cd07962 Anticodon_Ia_Val
630 764 InterPro IPR033705 Valyl tRNA synthetase, anticodon-binding domain
1 932 NCBIfam TIGR00422 valine--tRNA ligase
1 932 InterPro IPR002303 Valine-tRNA ligase
242 343 Gene3D G3DSA:3.90.740.10 -
242 343 InterPro IPR009008 Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain
201 241 Gene3D G3DSA:3.90.740.10 -
201 241 InterPro IPR009008 Valyl/Leucyl/Isoleucyl-tRNA synthetase, editing domain
469 490 PRINTS PR00986 Valyl-tRNA synthetase signature
469 490 InterPro IPR002303 Valine-tRNA ligase
35 46 PRINTS PR00986 Valyl-tRNA synthetase signature
35 46 InterPro IPR002303 Valine-tRNA ligase
236 253 PRINTS PR00986 Valyl-tRNA synthetase signature
236 253 InterPro IPR002303 Valine-tRNA ligase
500 518 PRINTS PR00986 Valyl-tRNA synthetase signature
500 518 InterPro IPR002303 Valine-tRNA ligase
369 382 PRINTS PR00986 Valyl-tRNA synthetase signature
369 382 InterPro IPR002303 Valine-tRNA ligase
204 355 FunFam G3DSA:3.90.740.10:FF:000021 Valine--tRNA ligase
3 200 FunFam G3DSA:3.40.50.620:FF:000032 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...

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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_A0A0H3GQW8
AlphaFold full sequence Viewing
ColabFold KP13_01303
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
18 0.226

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 19.3 0.837
2 8.67 0.463
3 3.52 0.129
4 3.25 0.113
5 2.76 0.084

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.

68 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](…
MRC P56690 500.6 Da LogP 2.59 TPSA 146.1 1 viol. ✓ Clean C[C@H]([C@H]1[C@@H](O1)C[C@H]2CO[C@H]([C@@H]([C…
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.