Protein profile

PA5334

ribonuclease PH

Genome: NC_002516.2

Gene: rph PA5334 Structure source: Experimental + AlphaFold UniProt P50597
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Amino acids 239
Annotations 8
Features 20
PDB binders 2
Druggability 0.62

Overview

Basic information about this protein and its source genome.

Accession
PA5334
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
rph PA5334
Status
annotated
Amino acids
239
Structure source
Experimental + AlphaFold
EC
2.7.7.56
GO
GO:0000175 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule. GO:0003723 Binding to an RNA molecule or a portion thereof. GO:0000049 Binding to a transfer RNA. GO:0009022 Catalysis of the reaction: tRNA(n+1) + phosphate = tRNA(n) + a nucleoside diphosphate. GO:0031125 Any process involved in forming the mature 3' end of an rRNA molecule. GO:0016075 The chemical reactions and pathways resulting in the breakdown of rRNA, ribosomal RNA, a structural constituent of ribosomes.

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
27.168
Human E-value
1.4e-08
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 0.62
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 7 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

7
  • GO:0000175 Catalysis of the sequential cleavage of mononucleotides from a free 3' terminus of an RNA molecule.
  • GO:0003723 Binding to an RNA molecule or a portion thereof.
  • GO:0000049 Binding to a transfer RNA.
  • GO:0009022 Catalysis of the reaction: tRNA(n+1) + phosphate = tRNA(n) + a nucleoside diphosphate.
  • GO:0031125 Any process involved in forming the mature 3' end of an rRNA molecule.
  • GO:0016075 The chemical reactions and pathways resulting in the breakdown of rRNA, ribosomal RNA, a structural constituent of ribosomes.
  • 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.

20 records
Show feature table
Start End DB Term Name
3 235 PANTHER PTHR11953 EXOSOME COMPLEX COMPONENT
3 237 NCBIfam TIGR01966 ribonuclease PH
3 237 InterPro IPR002381 Ribonuclease PH, bacterial-type
153 238 SUPERFAMILY SSF55666 Ribonuclease PH domain 2-like
153 238 InterPro IPR036345 Exoribonuclease, PH domain 2 superfamily
117 129 ProSitePatterns PS01277 Ribonuclease PH signature.
117 129 InterPro IPR018336 Ribonuclease PH, conserved site
3 182 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like
3 182 InterPro IPR020568 Ribosomal protein S5 domain 2-type fold
10 239 Gene3D G3DSA:3.30.230.70 -
10 239 InterPro IPR027408 PNPase/RNase PH domain superfamily
15 238 Hamap MF_00564 Ribonuclease PH [rph].
15 238 InterPro IPR002381 Ribonuclease PH, bacterial-type
10 238 FunFam G3DSA:3.30.230.70:FF:000003 Ribonuclease PH
11 141 Pfam PF01138 3' exoribonuclease family, domain 1
11 141 InterPro IPR001247 Exoribonuclease, phosphorolytic domain 1
11 237 CDD cd11362 RNase_PH_bact
11 237 InterPro IPR002381 Ribonuclease PH, bacterial-type
159 224 Pfam PF03725 3' exoribonuclease family, domain 2
159 224 InterPro IPR015847 Exoribonuclease, phosphorolytic domain 2

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

2 + 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 1R6L
X-ray 1.90 Å A
100.0% 1-239
PDBe RCSB PDBj File
Viewing
PDB 1R6M
X-ray 2.00 Å A
100.0% 1-239
PDBe RCSB PDBj File
Loaded
AlphaFold PA5334
AlphaFold — — 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
2 0.62
1 0.481

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 18.78 0.83

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.

52 records

Highest-confidence structural evidence: ligands co-crystallized with this exact protein. If the source PDB is loaded in TPW, use Open crystal to inspect it in the structure viewer.

Show only:
Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
NHE
1R6L 1.90 Å Open crystal
207.3 Da LogP 0.80 TPSA 66.4 ✓ Ro5 ✓ Clean C1CCC(CC1)NCCS(=O)(=O)O

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.