Protein profile

VK055_1847

YbeY

Genome: KpATCC43816

Gene: AIK80453.1 ybeY Structure source: AlphaFold + ColabFold UniProt A0A0H3GPX7
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Amino acids 157
Annotations 6
Features 13
PDB binders 0
Druggability 0.493

Overview

Basic information about this protein and its source genome.

Accession
VK055_1847
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
AIK80453.1 ybeY
Status
annotated
Amino acids
157
Structure source
AlphaFold + ColabFold
EC
3.1.-.-
GO
GO:0006364 Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules. GO:0004222 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:0004521 Catalysis of the cleavage of ester linkages within ribonucleic acid by creating internal breaks. GO:0008270 Binding to a zinc ion (Zn).

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Human identity (%)
0.0
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
89.172
DEG E-value
4.81e-102
Localization
Cytoplasmic
ColabFold pLDDT
93.88

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 0.493
Structure A0A0H3GPX7
Pocket Pocket 3
P2Rank 0.791
Structure A0A0H3GPX7
Pocket Pocket 1
ColabFold model
FPocket 0.447 · Pocket 1
P2Rank 0.821 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 182 / 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 5 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

5
  • GO:0006364 Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
  • GO:0004222 Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0004521 Catalysis of the cleavage of ester linkages within ribonucleic acid by creating internal breaks.
  • GO:0008270 Binding to a zinc ion (Zn).

Sequence Features

Domain/signature hits from InterPro and related databases.

13 records
Show feature table
Start End DB Term Name
16 147 NCBIfam TIGR00043 rRNA maturation RNase YbeY
16 147 InterPro IPR002036 Endoribonuclease YbeY
5 148 Hamap MF_00009 Endoribonuclease YbeY [ybeY].
5 148 InterPro IPR002036 Endoribonuclease YbeY
1 155 Gene3D G3DSA:3.40.390.30 Metalloproteases ("zincins"), catalytic domain
1 155 InterPro IPR023091 Metalloprotease catalytic domain superfamily, predicted
15 154 PANTHER PTHR46986 ENDORIBONUCLEASE YBEY, CHLOROPLASTIC
15 154 InterPro IPR002036 Endoribonuclease YbeY
114 124 ProSitePatterns PS01306 Uncharacterized protein family UPF0054 signature.
114 124 InterPro IPR020549 Endoribonuclease YbeY, conserved site
21 142 Pfam PF02130 Endoribonuclease YbeY
21 142 InterPro IPR002036 Endoribonuclease YbeY
3 151 SUPERFAMILY SSF55486 Metalloproteases ("zincins"), catalytic domain

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_A0A0H3GPX7
AlphaFold — — full sequence — Viewing
ColabFold VK055_1847
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
3 0.493

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 12.11 0.639