Protein profile

PA4944

RNA-binding protein Hfq

Genome: NC_002516.2

Gene: hfq PA4944 Structure source: Experimental + AlphaFold UniProt Q9HUM0
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Amino acids 82
Annotations 8
Features 15
PDB binders 5
Druggability 0.961

Overview

Basic information about this protein and its source genome.

Accession
PA4944
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
hfq PA4944
Status
annotated
Amino acids
82
Structure source
Experimental + AlphaFold
GO
GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes. GO:0003723 Binding to an RNA molecule or a portion thereof. GO:0009372 The cell-cell signaling process in which single-celled organisms carry out coordinated responses by monitoring their own population density, and often also that of other microbes, by producing small, diffusible, signal molecules, detecting the concentration of these molecules, and triggering a signal transduction pathway when a certain threshold is reached. Quorum sensing can occur amongst microbial communities in the environment or within host organisms. GO:0043609 Any process that modulates the frequency, rate, or extent of carbon utilization. GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription. GO:0043487 Any process that modulates the propensity of RNA molecules to degradation. Includes processes that both stabilize and destabilize RNAs.

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 0.961
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

8 GO

Gene Ontology (GO)

8
  • GO:0005829 The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
  • GO:0003723 Binding to an RNA molecule or a portion thereof.
  • GO:0009372 The cell-cell signaling process in which single-celled organisms carry out coordinated responses by monitoring their own population density, and often also that of other microbes, by producing small, diffusible, signal molecules, detecting the concentration of these molecules, and triggering a signal transduction pathway when a certain threshold is reached. Quorum sensing can occur amongst microbial communities in the environment or within host organisms.
  • GO:0043609 Any process that modulates the frequency, rate, or extent of carbon utilization.
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0043487 Any process that modulates the propensity of RNA molecules to degradation. Includes processes that both stabilize and destabilize RNAs.
  • GO:0006417 Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
  • GO:0045974 Any process, mediated by small non-coding RNAs, that modulates the frequency, rate or extent that mRNAs are effectively translated into protein.

Sequence Features

Domain/signature hits from InterPro and related databases.

15 records
Show feature table
Start End DB Term Name
6 64 CDD cd01716 Hfq
6 64 InterPro IPR005001 RNA-binding protein Hfq
1 76 PANTHER PTHR34772 RNA-BINDING PROTEIN HFQ
1 76 InterPro IPR005001 RNA-binding protein Hfq
6 64 NCBIfam TIGR02383 RNA chaperone Hfq
7 69 SUPERFAMILY SSF50182 Sm-like ribonucleoproteins
7 69 InterPro IPR010920 LSM domain superfamily
1 64 Hamap MF_00436 RNA-binding protein Hfq [hfq].
1 64 InterPro IPR005001 RNA-binding protein Hfq
9 68 ProSiteProfiles PS52002 Sm domain profile.
9 68 InterPro IPR047575 Sm domain
7 68 Pfam PF17209 Hfq protein
7 68 InterPro IPR005001 RNA-binding protein Hfq
1 82 Gene3D G3DSA:2.30.30.100 -
1 75 FunFam G3DSA:2.30.30.100:FF:000001 RNA-binding protein Hfq

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

12 + 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 1U1S
X-ray 1.60 Å A,B,C,D,E,F
100.0% 1-82
PDBe RCSB PDBj File
Viewing
PDB 3INZ
X-ray 1.70 Å A,B,C,D,E,F
100.0% 1-82
PDBe RCSB PDBj File
Loaded
PDB 4J6W
X-ray 1.80 Å A,B,C,D,E,F
100.0% 1-82
PDBe RCSB PDBj File
Loaded
PDB 4MML
X-ray 1.80 Å A
100.0% 1-82
PDBe RCSB PDBj File
Loaded
PDB 1U1T
X-ray 1.90 Å A,B,C,D,E,F
100.0% 1-82
PDBe RCSB PDBj File
Loaded
PDB 3QUI
X-ray 1.93 Å A,B,C,D,E,F
100.0% 1-82
PDBe RCSB PDBj File
Loaded
PDB 3M4G
X-ray 2.05 Å A,B,C,D,E,F,G,H,I,J,K,L
100.0% 1-82
PDBe RCSB PDBj File
Loaded
PDB 4J5Y
X-ray 2.10 Å A,B,C,D,E,F
100.0% 1-82
PDBe RCSB PDBj File
Loaded
PDB 4J6Y
X-ray 2.14 Å A,B,C,D,E,F
100.0% 1-82
PDBe RCSB PDBj File
Loaded
PDB 4MMK
X-ray 2.16 Å A,B,C,D,E,F,G,H,I,J,K,L
100.0% 1-82
PDBe RCSB PDBj File
Loaded
PDB 4J6X
X-ray 2.22 Å A,B,C,D,E,F
100.0% 1-82
PDBe RCSB PDBj File
Loaded
PDB 6XYJ
X-ray 2.77 Å AAA,BBB,CCC,DDD,EEE,FFF
100.0% 1-82
PDBe RCSB PDBj File
Metadata only
AlphaFold PA4944
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
1 0.961
2 0.888

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.

55 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
ADE
3QUI 1.93 Å Open crystal
135.1 Da LogP -0.06 TPSA 80.5 ✓ Ro5 ✓ Clean c1[nH]c2c(n1)c(ncn2)N
ANP
3QUI 1.93 Å Open crystal
506.2 Da LogP -2.06 TPSA 281.9 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…

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.