Protein profile

VK055_2086

cys-tRNAPro and Cys-tRNACys deacylase

Genome: KpATCC43816

Gene: AIK80691.1 ybaK Structure source: AlphaFold + ColabFold UniProt A0A0H3GKM0
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Amino acids 159
Annotations 5
Features 14
PDB binders 0
Druggability 0.843

Overview

Basic information about this protein and its source genome.

Accession
VK055_2086
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK80691.1 ybaK
Status
annotated
Amino acids
159
Structure source
AlphaFold + ColabFold
EC
4.2.-.-
GO
GO:0002161 The hydrolysis of an incorrectly aminoacylated tRNA. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring. GO:0006412 The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
N
DEG identity (%)
28.319
Localization
Cytoplasmic
ColabFold pLDDT
97.22

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 0.843
Structure A0A0H3GKM0
Pocket Pocket 1
P2Rank 0.391
Structure A0A0H3GKM0
Pocket Pocket 1
ColabFold model
FPocket 0.816 · Pocket 1
P2Rank 0.361 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 179 / 4744 genomes with a hit
Normalized 0.038

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 4 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

4
  • GO:0002161 The hydrolysis of an incorrectly aminoacylated tRNA.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0016829 Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
  • GO:0006412 The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.

Sequence Features

Domain/signature hits from InterPro and related databases.

14 records
Show feature table
Start End DB Term Name
1 159 PIRSF PIRSF006181 EbsC_YbaK
1 159 InterPro IPR004369 Prolyl-tRNA editing protein, YbaK/EbsC
31 146 Pfam PF04073 Aminoacyl-tRNA editing domain
31 146 InterPro IPR007214 YbaK/aminoacyl-tRNA synthetase-associated domain
10 157 PANTHER PTHR30411 UNCHARACTERIZED
2 156 NCBIfam TIGR00011 Cys-tRNA(Pro) deacylase
2 156 InterPro IPR004369 Prolyl-tRNA editing protein, YbaK/EbsC
2 155 SUPERFAMILY SSF55826 YbaK/ProRS associated domain
2 155 InterPro IPR036754 YbaK/aminoacyl-tRNA synthetase-associated domain superfamily
1 155 CDD cd00002 YbaK_deacylase
1 155 InterPro IPR004369 Prolyl-tRNA editing protein, YbaK/EbsC
1 159 Gene3D G3DSA:3.90.960.10 -
1 159 InterPro IPR036754 YbaK/aminoacyl-tRNA synthetase-associated domain superfamily
1 159 FunFam G3DSA:3.90.960.10:FF:000002 Cys-tRNA(Pro)/Cys-tRNA(Cys) deacylase

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

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_A0A0H3GKM0
AlphaFold — — full sequence — Viewing
ColabFold VK055_2086
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 0.843

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 4.46 0.189