Protein profile

PA2976

ribonuclease E

Genome: NC_002516.2

Gene: rne PA2976 Structure source: Experimental + AlphaFold UniProt Q9HZM8
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Amino acids 1057
Annotations 15
Features 30
PDB binders 1
Druggability 0.616

Overview

Basic information about this protein and its source genome.

Accession
PA2976
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
rne PA2976
Status
annotated
Amino acids
1057
Structure source
Experimental + AlphaFold
EC
3.1.26.12
GO
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: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:0019843 Binding to a ribosomal RNA.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
Y
Localization
Cytoplasmic

Selected Druggability evidence

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 0.616
Structure –
Pocket –

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: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: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: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.
  • 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:0003676 Binding to a nucleic acid.

Sequence Features

Domain/signature hits from InterPro and related databases.

30 records
Show feature table
Start End DB Term Name
36 116 Pfam PF00575 S1 RNA binding domain
36 116 InterPro IPR003029 S1 domain
399 509 Gene3D G3DSA:3.40.1260.20 Ribonuclease E, catalytic domain
1 1045 Hamap MF_00970 Ribonuclease E [rne].
1 1045 InterPro IPR028878 Ribonuclease E
13 422 NCBIfam TIGR00757 Rne/Rng family ribonuclease
13 422 InterPro IPR004659 Ribonuclease E/G
568 1057 MobiDBLite mobidb-lite consensus disorder prediction
31 123 FunFam G3DSA:2.40.50.140:FF:000040 Ribonuclease E
507 554 MobiDBLite mobidb-lite consensus disorder prediction
34 123 CDD cd04453 S1_RNase_E
39 117 ProSiteProfiles PS50126 S1 domain profile.
39 117 InterPro IPR003029 S1 domain
31 123 Gene3D G3DSA:2.40.50.140 -
31 123 InterPro IPR012340 Nucleic acid-binding, OB-fold
119 388 Pfam PF10150 Ribonuclease E/G family
119 388 InterPro IPR019307 RNA-binding protein AU-1/Ribonuclease E/G
817 855 MobiDBLite mobidb-lite consensus disorder prediction
398 509 FunFam G3DSA:3.40.1260.20:FF:000002 Ribonuclease E
958 978 Coils Coil Coil
1036 1057 MobiDBLite mobidb-lite consensus disorder prediction
952 971 MobiDBLite mobidb-lite consensus disorder prediction
314 334 Coils Coil Coil
37 117 SMART SM00316 S1_6
37 117 InterPro IPR022967 RNA-binding domain, S1
40 123 SUPERFAMILY SSF50249 Nucleic acid-binding proteins
40 123 InterPro IPR012340 Nucleic acid-binding, OB-fold
1 517 PANTHER PTHR30001 RIBONUCLEASE
1 517 InterPro IPR004659 Ribonuclease E/G
581 732 MobiDBLite mobidb-lite consensus disorder prediction

3D Structure

Selected loaded structure. Experimental PDB entries may cover only a portion of the sequence; predicted models typically cover the full protein.

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Structural evidence

1 + 1

Experimental PDB entries and predicted models. Click Switch to display a different structure in the viewer.

Entry Method Resolution Chain Coverage Links Status
PDB 5FT1
X-ray 2.75 Å C,D,F,H,J,L
1.9% 756-775
PDBe RCSB PDBj File
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AlphaFold PA2976
AlphaFold — — full sequence — Loaded
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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.