Protein profile

KP13_02199

Lysyl-tRNA synthetase

Genome: KpKP13

Gene: AHE42768.1 lysS Structure source: AlphaFold + ColabFold UniProt A0A0H3H2L3
Amino acids 505
Annotations 13
Features 38
PDB binders 18
Druggability 0.799

Overview

Basic information about this protein and its source genome.

Accession
KP13_02199
Gene
AHE42768.1 lysS
Status
annotated
Amino acids
505
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
53.75
Human E-value
2.09e-18
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
94.653
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
94.19

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 0.799
Structure A0A0H3H2L3
Pocket Pocket 1
P2Rank 0.947
Structure A0A0H3H2L3
Pocket Pocket 1
ColabFold model
FPocket 0.659 · Pocket 1
P2Rank 0.923 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 1485 / 4744 genomes with a hit
Normalized 0.313

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 12 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

12
  • 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:0003676 Binding to a nucleic acid.
  • GO:0006430 The process of coupling lysine to lysyl-tRNA, catalyzed by lysyl-tRNA synthetase. The lysyl-tRNA synthetase is a class-II synthetase. The activated amino acid is transferred to the 3'-OH group of a lysine-accetping tRNA.
  • 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:0004824 Catalysis of the reaction: ATP + L-lysine + tRNA(Lys) = AMP + diphosphate + L-lysyl-tRNA(Lys).
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0042803 Binding to an identical protein to form a homodimer.
  • GO:0000049 Binding to a transfer RNA.

Sequence Features

Domain/signature hits from InterPro and related databases.

38 records
Show feature table
Start End DB Term Name
12 32 Coils Coil Coil
155 501 Gene3D G3DSA:3.30.930.10 Bira Bifunctional Protein; Domain 2
155 501 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
262 279 PRINTS PR00982 Lysyl-tRNA synthetase signature
262 279 InterPro IPR018149 Lysyl-tRNA synthetase, class II, C-terminal
215 231 PRINTS PR00982 Lysyl-tRNA synthetase signature
215 231 InterPro IPR018149 Lysyl-tRNA synthetase, class II, C-terminal
199 209 PRINTS PR00982 Lysyl-tRNA synthetase signature
199 209 InterPro IPR018149 Lysyl-tRNA synthetase, class II, C-terminal
244 257 PRINTS PR00982 Lysyl-tRNA synthetase signature
244 257 InterPro IPR018149 Lysyl-tRNA synthetase, class II, C-terminal
386 402 PRINTS PR00982 Lysyl-tRNA synthetase signature
386 402 InterPro IPR018149 Lysyl-tRNA synthetase, class II, C-terminal
184 503 ProSiteProfiles PS50862 Aminoacyl-transfer RNA synthetases class-II family profile.
184 503 InterPro IPR006195 Aminoacyl-tRNA synthetase, class II
67 174 CDD cd04322 LysRS_N
67 174 InterPro IPR044136 Lysine-tRNA ligase, class II, N-terminal
177 503 CDD cd00775 LysRS_core
177 503 InterPro IPR018149 Lysyl-tRNA synthetase, class II, C-terminal
68 146 Pfam PF01336 OB-fold nucleic acid binding domain
68 146 InterPro IPR004365 OB-fold nucleic acid binding domain, AA-tRNA synthetase-type
21 505 Hamap MF_00252 Lysine--tRNA ligase [lysS].
21 505 InterPro IPR002313 Lysine-tRNA ligase, class II
13 155 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
13 155 InterPro IPR012340 Nucleic acid-binding, OB-fold
15 155 FunFam G3DSA:2.40.50.140:FF:000024 Lysine--tRNA ligase
162 502 SUPERFAMILY SSF55681 Class II aaRS and biotin synthetases
162 502 InterPro IPR045864 Class II Aminoacyl-tRNA synthetase/Biotinyl protein ligase (BPL) and lipoyl protein ligase (LPL)
162 501 Pfam PF00152 tRNA synthetases class II (D, K and N)
162 501 InterPro IPR004364 Aminoacyl-tRNA synthetase, class II (D/K/N)
1 505 PIRSF PIRSF039101 LysRS2
1 505 InterPro IPR034762 Bacterial/eukaryotic lysine-tRNA ligase, class II
14 505 NCBIfam TIGR00499 lysine--tRNA ligase
14 505 InterPro IPR002313 Lysine-tRNA ligase, class II
15 154 Gene3D G3DSA:2.40.50.140 -
15 154 InterPro IPR012340 Nucleic acid-binding, OB-fold
4 505 PANTHER PTHR42918 LYSYL-TRNA SYNTHETASE
156 501 FunFam G3DSA:3.30.930.10:FF:000001 Lysine--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_A0A0H3H2L3
AlphaFold full sequence Viewing
ColabFold KP13_02199
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 0.799
23 0.467

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 27.46 0.921
2 2.25 0.056
3 1.15 0.009

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.

70 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
45A Q15046 345.3 Da LogP -1.14 TPSA 165.8 ✓ Ro5 ✓ Clean CP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@@H](O1)n2cnc3c…
9X0 Q8IDJ8 285.3 Da LogP 3.10 TPSA 59.3 ✓ Ro5 ✓ Clean c1ccc2c(c1)C(=O)C=C(O2)C(=O)NCC3CCCCC3
ACP P0A8N5 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ADN Q5CR27 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)…
APC Q15046 505.2 Da LogP -1.52 TPSA 269.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
B4P P0A8N5 836.4 Da LogP -2.45 TPSA 434.0 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
D4O W7JP72 290.4 Da LogP 3.40 TPSA 66.8 ✓ Ro5 ✓ Clean C[C@H]1CCC[C@@H](C1)C[C@H]2Cc3cc(cc(c3C(=O)O2)O…
D4U W7JP72 276.3 Da LogP 3.15 TPSA 66.8 ✓ Ro5 ✓ Clean c1c(cc(c2c1C[C@@H](OC2=O)CC3CCCCC3)O)O
D4X W7JP72 289.4 Da LogP 2.97 TPSA 69.6 ✓ Ro5 ✓ Clean C[C@H]1CCC[C@@H](C1)C[C@H]2Cc3cc(cc(c3C(=O)N2)O…
D5F W7JP72 288.3 Da LogP 3.57 TPSA 70.7 ✓ Ro5 ✓ Clean C[C@H]1CCC[C@@H](C1)CC2=Cc3cc(cc(c3C(=O)O2)O)O
D5O W7JP72 274.3 Da LogP 3.33 TPSA 70.7 ✓ Ro5 ✓ Clean c1c(cc(c2c1C=C(OC2=O)CC3CCCCC3)O)O
EZ3 Q8IDJ8 308.3 Da LogP 1.50 TPSA 96.2 ✓ Ro5 ✓ Clean C[C@H]1CCC[C@@H](O1)[C@H]([C@H]2Cc3cc(cc(c3C(=O…
F6O Q8IDJ8 580.8 Da LogP 3.77 TPSA 115.8 2 viol. ✓ Clean CC(C)S(=O)(=O)c1ccccc1Nc2ncnc(n2)Nc3ccc(cc3OC)N…
FYB Q8IDJ8 355.3 Da LogP 2.60 TPSA 79.5 ✓ Ro5 ✓ Clean c1cc2c(cc1F)C(=O)C=C(O2)C(=O)NCC3(CCC(CC3)(F)F)O
KAA Q9RHV9 474.5 Da LogP -3.14 TPSA 243.8 2 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
KRS Q8IDJ8 292.3 Da LogP 2.53 TPSA 76.0 ✓ Ro5 ✓ Clean C[C@H]1CCC[C@@H](O1)C[C@H]2Cc3cc(cc(c3C(=O)O2)O…
LYN Q9RHV9 146.2 Da LogP -1.79 TPSA 96.8 ✓ Ro5 ✓ Clean C(CC[NH3+])C[C@@H](C(=O)N)N
XAH Q9RHV9 490.4 Da LogP -2.35 TPSA 256.2 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.