Protein profile

VK055_4850

ribonuclease Z

Genome: KpATCC43816

Gene: rnz AIK83377.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GR46
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Amino acids 306
Annotations 7
Features 16
PDB binders 0
Druggability 0.3

Overview

Basic information about this protein and its source genome.

Accession
VK055_4850
Assembly
Klebsiella pneumoniae subsp. pneumoniae strain ATCC 43816 KPPR1, complete genome
Gene
rnz AIK83377.1
Status
annotated
Amino acids
306
Structure source
AlphaFold + ColabFold
EC
3.1.-.-
GO
GO:0016891 Catalysis of the hydrolysis of ester linkages within ribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters. GO:0042779 OBSOLETE. Cleavage of the 3'-end of the pre-tRNA as part of the process of generating the mature 3'-end of the tRNA; may involve endonucleolytic or exonucleolytic cleavage, or both. GO:0042781 Catalysis of the endonucleolytic cleavage of RNA, removing extra 3' nucleotides from tRNA precursor, generating 3' termini of tRNAs. A 3'-hydroxy group is left at the tRNA terminus and a 5'-phosphoryl group is left at the trailer molecule. GO:0004527 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end. GO:0042802 Binding to an identical protein or proteins. GO:0008270 Binding to a zinc ion (Zn).

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
46.0
Human E-value
3.45e-08
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
48.026
DEG E-value
1.71e-104
Localization
Cytoplasmic
ColabFold pLDDT
95.64

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 0.3
Structure A0A0H3GR46
Pocket Pocket 4
P2Rank 0.572
Structure A0A0H3GR46
Pocket Pocket 1
ColabFold model
FPocket 0.311 · Pocket 2
P2Rank 0.67 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 111 / 4744 genomes with a hit
Normalized 0.023

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 6 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

6
  • GO:0016891 Catalysis of the hydrolysis of ester linkages within ribonucleic acids by creating internal breaks to yield 5'-phosphomonoesters.
  • GO:0042779 OBSOLETE. Cleavage of the 3'-end of the pre-tRNA as part of the process of generating the mature 3'-end of the tRNA; may involve endonucleolytic or exonucleolytic cleavage, or both.
  • GO:0042781 Catalysis of the endonucleolytic cleavage of RNA, removing extra 3' nucleotides from tRNA precursor, generating 3' termini of tRNAs. A 3'-hydroxy group is left at the tRNA terminus and a 5'-phosphoryl group is left at the trailer molecule.
  • GO:0004527 Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
  • GO:0042802 Binding to an identical protein or proteins.
  • GO:0008270 Binding to a zinc ion (Zn).

Sequence Features

Domain/signature hits from InterPro and related databases.

16 records
Show feature table
Start End DB Term Name
3 303 CDD cd07717 RNaseZ_ZiPD-like_MBL-fold
3 303 InterPro IPR013471 Ribonuclease Z/BN
1 304 SUPERFAMILY SSF56281 Metallo-hydrolase/oxidoreductase
1 304 InterPro IPR036866 Ribonuclease Z/Hydroxyacylglutathione hydrolase-like
2 304 NCBIfam TIGR02651 ribonuclease Z
2 304 InterPro IPR013471 Ribonuclease Z/BN
36 153 Pfam PF12706 Beta-lactamase superfamily domain
36 153 InterPro IPR001279 Metallo-beta-lactamase
202 271 Pfam PF12706 Beta-lactamase superfamily domain
202 271 InterPro IPR001279 Metallo-beta-lactamase
1 305 PANTHER PTHR46018 ZINC PHOSPHODIESTERASE ELAC PROTEIN 1
1 305 FunFam G3DSA:3.60.15.10:FF:000002 Ribonuclease Z
1 305 Hamap MF_01818 Ribonuclease BN [rbn].
1 305 InterPro IPR013471 Ribonuclease Z/BN
1 305 Gene3D G3DSA:3.60.15.10 -
1 305 InterPro IPR036866 Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

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_A0A0H3GR46
AlphaFold — — full sequence — Viewing
ColabFold VK055_4850
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
4 0.3

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 9.18 0.491
2 1.02 0.006