Protein profile

VK055_4762

glutamate--tRNA ligase

Genome: KpATCC43816

Gene: gltX AIK83292.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GTA8
Amino acids 472
Annotations 11
Features 32
PDB binders 10
Druggability 0.394

Overview

Basic information about this protein and its source genome.

Accession
VK055_4762
Gene
gltX AIK83292.1
Status
annotated
Amino acids
472
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
36.364
Human E-value
3.48e-65
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
95.532
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
95.9

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 0.394
Structure A0A0H3GTA8
Pocket Pocket 3
P2Rank 0.907
Structure A0A0H3GTA8
Pocket Pocket 1
ColabFold model
FPocket 0.53 · Pocket 4
P2Rank 0.866 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 192 / 4744 genomes with a hit
Normalized 0.04

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 10 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

10
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0043039 The chemical reactions and pathways by which the various amino acids become bonded to their corresponding tRNAs. The most common route for synthesis of aminoacyl tRNA is 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, usually catalyzed by the cognate aminoacyl-tRNA ligase. A given aminoacyl-tRNA ligase aminoacylates all species of an isoaccepting group of tRNA molecules.
  • GO:0006424 The process of coupling glutamate to glutamyl-tRNA, catalyzed by glutamyl-tRNA synthetase. The glutamyl-tRNA synthetase is a class-I synthetase. The activated amino acid is transferred to the 2'-OH group of a glutamic acid-accetping tRNA. The 2'-O-aminoacyl-tRNA will ultimately migrate to the 3' position via transesterification.
  • GO:0004818 Catalysis of the reaction: ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu).
  • GO:0008270 Binding to a zinc ion (Zn).
  • GO:0004812 Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
  • 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: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:0000049 Binding to a transfer RNA.
  • 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.

32 records
Show feature table
Start End DB Term Name
326 461 Pfam PF19269 Anticodon binding domain
326 461 InterPro IPR045462 Aminoacyl-tRNA synthetase, class I, anticodon-binding
2 462 PANTHER PTHR43311 GLUTAMATE--TRNA LIGASE
363 471 Gene3D G3DSA:1.10.10.350 -
363 471 InterPro IPR020751 Aminoacyl-tRNA synthetase, class I, anticodon-binding domain, subdomain 2
1 313 Gene3D G3DSA:3.40.50.620 HUPs
1 313 InterPro IPR014729 Rossmann-like alpha/beta/alpha sandwich fold
2 463 NCBIfam TIGR00464 glutamate--tRNA ligase
2 463 InterPro IPR004527 Glutamate-tRNA ligase, bacterial/mitochondrial
6 18 PRINTS PR00987 Glutamyl-tRNA synthetase signature
6 18 InterPro IPR000924 Glutamyl/glutaminyl-tRNA synthetase
179 189 PRINTS PR00987 Glutamyl-tRNA synthetase signature
179 189 InterPro IPR000924 Glutamyl/glutaminyl-tRNA synthetase
20 31 PRINTS PR00987 Glutamyl-tRNA synthetase signature
20 31 InterPro IPR000924 Glutamyl/glutaminyl-tRNA synthetase
195 203 PRINTS PR00987 Glutamyl-tRNA synthetase signature
195 203 InterPro IPR000924 Glutamyl/glutaminyl-tRNA synthetase
35 48 PRINTS PR00987 Glutamyl-tRNA synthetase signature
35 48 InterPro IPR000924 Glutamyl/glutaminyl-tRNA synthetase
2 313 CDD cd00808 GluRS_core
2 313 InterPro IPR033910 Glutamyl-tRNA synthetase
3 298 SUPERFAMILY SSF52374 Nucleotidylyl transferase
2 461 Hamap MF_00022 Glutamate--tRNA ligase [gltX].
2 461 InterPro IPR004527 Glutamate-tRNA ligase, bacterial/mitochondrial
9 20 ProSitePatterns PS00178 Aminoacyl-transfer RNA synthetases class-I signature.
9 20 InterPro IPR001412 Aminoacyl-tRNA synthetase, class I, conserved site
2 305 Pfam PF00749 tRNA synthetases class I (E and Q), catalytic domain
2 305 InterPro IPR020058 Glutamyl/glutaminyl-tRNA synthetase, class Ib, catalytic domain
299 461 SUPERFAMILY SSF48163 An anticodon-binding domain of class I aminoacyl-tRNA synthetases
299 461 InterPro IPR008925 Aminoacyl-tRNA synthetase, class I, anticodon-binding superfamily
363 471 FunFam G3DSA:1.10.10.350:FF:000001 Glutamate--tRNA ligase
1 314 FunFam G3DSA:3.40.50.620:FF:000007 Glutamate--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_A0A0H3GTA8
AlphaFold full sequence Viewing
ColabFold VK055_4762
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
2 0.269
1 0.117
4 0.012
31 0.0

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 31.04 0.907
2 3.28 0.091
3 2.77 0.068
4 1.56 0.019
5 1.24 0.01

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.

63 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
8X1 P07814 429.4 Da LogP -3.23 TPSA 203.8 1 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
91Y P07814 364.4 Da LogP 2.89 TPSA 84.0 ✓ Ro5 ✓ Clean c1ccc2c(c1)CC(C2)NC(=O)c3c(nccn3)NC(=O)C4CCCCC4
ADN P07814 267.2 Da LogP -1.98 TPSA 139.5 ✓ Ro5 ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ANP P07814 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)…
DTT P13188 154.3 Da LogP -0.43 TPSA 40.5 ✓ Ro5 ✓ Clean C([C@@H]([C@H](CS)O)O)S
GAU P27000 133.1 Da LogP -0.83 TPSA 83.5 ✓ Ro5 ✓ Clean C(CC(=O)O)[C@@H](CO)N
GOM P27000 461.3 Da LogP -4.33 TPSA 245.7 1 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
GSU P27000 475.4 Da LogP -3.40 TPSA 255.1 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
HFG P07814 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](…
QSI P00962 474.5 Da LogP -4.00 TPSA 260.9 2 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.