Protein profile

PA4581

transcriptional regulator RtcR

Genome: NC_002516.2

Gene: PA4581 rtcR Structure source: AlphaFold UniProt Q9HVK3
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Amino acids 531
Annotations 9
Features 27
PDB binders 6
Druggability 0.559

Overview

Basic information about this protein and its source genome.

Accession
PA4581
Assembly
Pseudomonas aeruginosa PAO1, complete genome
Gene
PA4581 rtcR
Status
annotated
Amino acids
531
Structure source
AlphaFold
GO
GO:0032993 A macromolecular complex containing both protein and DNA molecules. GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator. GO:0000987 Binding to a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site, located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by some RNA polymerase. Cis-regulatory sites are often referred to as a sequence motifs, enhancers, or silencers. GO:0001216 A DNA-binding transcription factor activity that activates or increases transcription of specific gene sets. GO:0045893 Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription. GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.

Target profile

Computed evidence for target prioritization.

Human off-target
No hit
Gut microbiome off-target
hit
Essential (DEG)
N
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 0.559
Structure –
Pocket –

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

9 GO

Gene Ontology (GO)

9
  • GO:0032993 A macromolecular complex containing both protein and DNA molecules.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0000987 Binding to a specific upstream regulatory DNA sequence (transcription factor recognition sequence or binding site, located in cis relative to the transcription start site (i.e., on the same strand of DNA) of a gene transcribed by some RNA polymerase. Cis-regulatory sites are often referred to as a sequence motifs, enhancers, or silencers.
  • GO:0001216 A DNA-binding transcription factor activity that activates or increases transcription of specific gene sets.
  • GO:0045893 Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0016887 Catalysis of the reaction: ATP + H2O = ADP + H+ phosphate. ATP hydrolysis is used in some reactions as an energy source, for example to catalyze a reaction or drive transport against a concentration gradient.
  • GO:0003700 A transcription regulator activity that modulates transcription of gene sets via selective and non-covalent binding to a specific double-stranded genomic DNA sequence (sometimes referred to as a motif) within a cis-regulatory region. Regulatory regions include promoters (proximal and distal) and enhancers. Genes are transcriptional units, and include bacterial operons.
  • GO:0008134 Binding to a transcription factor, a protein required to initiate or regulate transcription.

Sequence Features

Domain/signature hits from InterPro and related databases.

27 records
Show feature table
Start End DB Term Name
4 14 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide.
157 524 PANTHER PTHR32071 TRANSCRIPTIONAL REGULATORY PROTEIN
366 446 Gene3D G3DSA:1.10.8.60 -
190 358 Pfam PF00158 Sigma-54 interaction domain
190 358 InterPro IPR002078 RNA polymerase sigma factor 54 interaction domain
2 188 Pfam PF06956 Regulator of RNA terminal phosphate cyclase
2 188 InterPro IPR009715 Regulator of RNA terminal phosphate cyclase
15 20 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide.
190 441 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases
190 441 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
175 364 Gene3D G3DSA:3.40.50.300 -
175 364 InterPro IPR027417 P-loop containing nucleoside triphosphate hydrolase
1 3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide.
175 364 FunFam G3DSA:3.40.50.300:FF:001653 Transcriptional regulator RtcR
1 531 PIRSF PIRSF037354 RtcR
1 531 InterPro IPR017183 Sigma54-dependent transcriptional activator, RtcR
203 356 CDD cd00009 AAA
21 531 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region.
210 356 SMART SM00382 AAA_5
210 356 InterPro IPR003593 AAA+ ATPase domain
1 530 NCBIfam NF038308 RNA repair transcriptional activator RtcR
1 530 InterPro IPR017183 Sigma54-dependent transcriptional activator, RtcR
279 294 ProSitePatterns PS00676 Sigma-54 interaction domain ATP-binding region B signature.
279 294 InterPro IPR025943 Sigma-54 interaction domain, ATP-binding site 2
1 20 Phobius SIGNAL_PEPTIDE Signal peptide region
189 427 ProSiteProfiles PS50045 Sigma-54 interaction domain profile.
189 427 InterPro IPR002078 RNA polymerase sigma factor 54 interaction domain

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

0 + 1

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA4581
AlphaFold — — full sequence — Viewing
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 0.559
2 0.342

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.

56 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
08T
4LZZ
O67198 — — — [Be](OP(=O)(O)OP(=O)(O)OC[C@@H]1[C@H]([C@H]([C@…
5QT
5EP3
Q1ZS18 272.3 Da LogP 0.83 TPSA 99.9 ✓ Ro5 ✓ Clean CC(C)(C)COC(=O)CNC1=NNC(=O)NC1=S
AGS
5EXS
G3XCV0 523.2 Da LogP -1.51 TPSA 262.1 3 viol. ✓ Clean c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)…
ANP
4QHT
A0A0H3AHP1 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)…
AZU
5EP2
Q1ZS18 273.3 Da LogP 0.14 TPSA 104.9 ✓ Ro5 ✓ Clean CC(C)(C)COC(=O)CSC1=NNC(=O)NC1=O
C2E
5EXX
G3XCV0 690.4 Da LogP -3.05 TPSA 349.6 3 viol. ✓ Clean c1nc2c(n1[C@H]3[C@@H]([C@H]4[C@H](O3)CO[P@@](=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.