Protein profile

KP13_05431

Exoribonuclease 2

Genome: KpKP13

Gene: rnb AHE44978.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3GW65
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Amino acids 644
Annotations 9
Features 37
PDB binders 0
Druggability 0.466

Overview

Basic information about this protein and its source genome.

Accession
KP13_05431
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
rnb AHE44978.1
Status
annotated
Amino acids
644
Structure source
AlphaFold + ColabFold
EC
3.1.13.1
GO
GO:0003676 Binding to a nucleic acid. GO:0008859 Catalysis of the reaction: RNA + H2O = 5'-phosphomononucleotides. Cleaves RNA in the 3' to 5' direction. GO:0016070 The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. GO:0003723 Binding to an RNA molecule or a portion thereof. GO:0006401 The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage. GO:0004540 Catalysis of the cleavage of phosphodiester bonds in chains of RNA.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
37.079
Human E-value
2.3e-09
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
90.047
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
94.69

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 0.466
Structure A0A0H3GW65
Pocket Pocket 3
P2Rank 0.395
Structure A0A0H3GW65
Pocket Pocket 1
ColabFold model
FPocket 0.698 · Pocket 50
P2Rank 0.459 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 140 / 4744 genomes with a hit
Normalized 0.03

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0003676 Binding to a nucleic acid.
  • GO:0008859 Catalysis of the reaction: RNA + H2O = 5'-phosphomononucleotides. Cleaves RNA in the 3' to 5' direction.
  • GO:0016070 The cellular chemical reactions and pathways involving RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
  • GO:0003723 Binding to an RNA molecule or a portion thereof.
  • GO:0006401 The chemical reactions and pathways resulting in the breakdown of RNA, ribonucleic acid, one of the two main type of nucleic acid, consisting of a long, unbranched macromolecule formed from ribonucleotides joined in 3',5'-phosphodiester linkage.
  • GO:0004540 Catalysis of the cleavage of phosphodiester bonds in chains of RNA.
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0006402 The chemical reactions and pathways resulting in the breakdown of mRNA, messenger RNA, which is responsible for carrying the coded genetic 'message', transcribed from DNA, to sites of protein assembly at the ribosomes.

Sequence Features

Domain/signature hits from InterPro and related databases.

37 records
Show feature table
Start End DB Term Name
558 644 FunFam G3DSA:2.40.50.140:FF:000081 Exoribonuclease 2
1 82 Gene3D G3DSA:2.40.50.140 -
1 82 InterPro IPR012340 Nucleic acid-binding, OB-fold
8 80 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
8 80 InterPro IPR012340 Nucleic acid-binding, OB-fold
558 644 Gene3D G3DSA:2.40.50.140 -
558 644 InterPro IPR012340 Nucleic acid-binding, OB-fold
99 175 Pfam PF17876 Cold shock domain
99 175 InterPro IPR040476 RNase II/RNase R, cold shock domain
176 556 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
176 556 InterPro IPR012340 Nucleic acid-binding, OB-fold
1 643 Hamap MF_01036 Exoribonuclease 2 [rnb].
1 643 InterPro IPR011804 Ribonuclease II
484 508 ProSitePatterns PS01175 Ribonuclease II family signature.
484 508 InterPro IPR022966 Ribonuclease II/R, conserved site
23 79 SMART SM00357 csp_8
23 79 InterPro IPR011129 Cold shock domain
83 155 Gene3D G3DSA:2.40.50.640 -
1 642 NCBIfam TIGR02062 exoribonuclease II
1 642 InterPro IPR011804 Ribonuclease II
1 82 FunFam G3DSA:2.40.50.140:FF:000079 Exoribonuclease 2
83 171 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
83 171 InterPro IPR012340 Nucleic acid-binding, OB-fold
6 641 NCBIfam TIGR00358 VacB/RNase II family 3'-5' exoribonuclease
6 641 InterPro IPR004476 Ribonuclease II/ribonuclease R
560 636 Pfam PF00575 S1 RNA binding domain
560 636 InterPro IPR003029 S1 domain
184 637 PANTHER PTHR23355 RIBONUCLEASE
189 516 Pfam PF00773 RNB domain
189 516 InterPro IPR001900 Ribonuclease II/R
560 641 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
560 641 InterPro IPR012340 Nucleic acid-binding, OB-fold
189 517 SMART SM00955 RNB_2
189 517 InterPro IPR001900 Ribonuclease II/R
83 155 FunFam G3DSA:2.40.50.640:FF:000001 Exoribonuclease 2
24 80 Pfam PF08206 Ribonuclease B OB domain
24 80 InterPro IPR013223 Ribonuclease B, N-terminal OB 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_A0A0H3GW65
AlphaFold — — full sequence — Viewing
ColabFold KP13_05431
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 0.466
40 0.326
26 0.215

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 4.66 0.203
2 3.46 0.125
3 3.2 0.11
4 2.58 0.073
5 2.53 0.071