Protein profile

KP13_04926

Ribonuclease E

Genome: KpKP13

Gene: AHE45289.1 rne Structure source: AlphaFold + ColabFold UniProt A0A0H3GLF7
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Amino acids 1077
Annotations 15
Features 32
PDB binders 1
Druggability 0.832

Overview

Basic information about this protein and its source genome.

Accession
KP13_04926
Assembly
Klebsiella pneumoniae subsp. pneumoniae Kp13, complete sequence
Gene
AHE45289.1 rne
Status
annotated
Amino acids
1077
Structure source
AlphaFold + ColabFold
EC
3.1.26.12
GO
GO:0003676 Binding to a nucleic acid. GO:0006396 Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules. GO:0003723 Binding to an RNA molecule or a portion thereof. GO:0008995 Catalysis of the cleavage of single-stranded RNA that is monophosphorylated at its 5'-end; cleavage occurs predominantly at 5 nucleotides from the 5'-end and in A + U-rich regions, and is blocked by the presence of a 5'-triphosphate group. GO:0004540 Catalysis of the cleavage of phosphodiester bonds in chains of RNA. GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 (%)
74.864
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
62.09

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 0.832
Structure A0A0H3GLF7
Pocket Pocket 68
P2Rank 0.761
Structure A0A0H3GLF7
Pocket Pocket 1
ColabFold model
FPocket 0.769 · Pocket 2
P2Rank 0.88 · Pocket 1
Core conservation Accessory gene
Roary core
CoreCruncher accessory
Gut microbiome 107 / 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 14 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

14
  • GO:0003676 Binding to a nucleic acid.
  • GO:0006396 Any process involved in the conversion of one or more primary RNA transcripts into one or more mature RNA molecules.
  • GO:0003723 Binding to an RNA molecule or a portion thereof.
  • GO:0008995 Catalysis of the cleavage of single-stranded RNA that is monophosphorylated at its 5'-end; cleavage occurs predominantly at 5 nucleotides from the 5'-end and in A + U-rich regions, and is blocked by the presence of a 5'-triphosphate group.
  • GO:0004540 Catalysis of the cleavage of phosphodiester bonds in chains of RNA.
  • GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:0009898 The leaflet of the plasma membrane that faces the cytoplasm, including any protein embedded in, attached to, or peripherally associated with it.
  • GO:0000287 Binding to a magnesium (Mg) ion.
  • GO:0019843 Binding to a ribosomal RNA.
  • GO:0000049 Binding to a transfer RNA.
  • GO:0008270 Binding to a zinc ion (Zn).
  • 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.
  • GO:0006364 Any process involved in the conversion of a primary ribosomal RNA (rRNA) transcript into one or more mature rRNA molecules.
  • GO:0008033 The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.

Sequence Features

Domain/signature hits from InterPro and related databases.

32 records
Show feature table
Start End DB Term Name
37 119 SMART SM00316 S1_6
37 119 InterPro IPR022967 RNA-binding domain, S1
121 391 Pfam PF10150 Ribonuclease E/G family
121 391 InterPro IPR019307 RNA-binding protein AU-1/Ribonuclease E/G
401 510 Gene3D G3DSA:3.40.1260.20 Ribonuclease E, catalytic domain
508 537 MobiDBLite mobidb-lite consensus disorder prediction
1 1063 Hamap MF_00970 Ribonuclease E [rne].
1 1063 InterPro IPR028878 Ribonuclease E
31 125 FunFam G3DSA:2.40.50.140:FF:000040 Ribonuclease E
36 118 Pfam PF00575 S1 RNA binding domain
36 118 InterPro IPR003029 S1 domain
1047 1077 MobiDBLite mobidb-lite consensus disorder prediction
39 119 ProSiteProfiles PS50126 S1 domain profile.
39 119 InterPro IPR003029 S1 domain
508 524 MobiDBLite mobidb-lite consensus disorder prediction
1038 1074 Pfam PF12111 Polyribonucleotide phosphorylase C terminal
1038 1074 InterPro IPR021968 Polyribonucleotide phosphorylase C-terminal
693 713 Coils Coil Coil
768 827 MobiDBLite mobidb-lite consensus disorder prediction
1 517 PANTHER PTHR30001 RIBONUCLEASE
1 517 InterPro IPR004659 Ribonuclease E/G
590 742 MobiDBLite mobidb-lite consensus disorder prediction
401 510 FunFam G3DSA:3.40.1260.20:FF:000002 Ribonuclease E
31 125 Gene3D G3DSA:2.40.50.140 -
31 125 InterPro IPR012340 Nucleic acid-binding, OB-fold
788 803 MobiDBLite mobidb-lite consensus disorder prediction
590 734 MobiDBLite mobidb-lite consensus disorder prediction
40 124 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
40 124 InterPro IPR012340 Nucleic acid-binding, OB-fold
32 124 CDD cd04453 S1_RNase_E
13 425 NCBIfam TIGR00757 Rne/Rng family ribonuclease
13 425 InterPro IPR004659 Ribonuclease E/G

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_A0A0H3GLF7
AlphaFold — — full sequence — Viewing
ColabFold KP13_04926
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
68 0.832
32 0.811

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 12.1 0.639
2 3.09 0.103
3 2.18 0.052
4 1.63 0.027
5 1.59 0.025

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.

51 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
U
6G63
P21513 324.2 Da LogP -2.73 TPSA 171.3 ✓ Ro5 ✓ Clean C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)C…

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.