Protein profile

PA0576

RNA polymerase sigma factor RpoD

Genome: NC_002516.2

Gene: PA0576 rpoDA rpoD Structure source: AlphaFold UniProt P26480
Amino acids 617
Annotations 9
Features 54
PDB binders 12
Druggability 0.501

Overview

Basic information about this protein and its source genome.

Accession
PA0576
Gene
PA0576 rpoDA rpoD
Status
annotated
Amino acids
617
Structure source
AlphaFold
GO
GO:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures. GO:1903865 A protein complex which is capable of sigma factor antagonist activity. GO:0003899 Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'. GO:0016987 Sigma factors act as the promoter specificity subunit of eubacterial and plant plastid multisubunit RNA polymerases, whose core subunit composition is often described as alpha(2)-beta-beta-prime. Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, the sigma factor binds specifically to promoter elements. The sigma subunit is released once elongation begins. GO:0000976 Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon. GO:0006352 The initial step of transcription, consisting of the assembly of the RNA polymerase preinitiation complex (PIC) at a gene promoter, as well as the formation of the first few bonds of the RNA transcript. Transcription initiation includes abortive initiation events, which occur when the first few nucleotides are repeatedly synthesized and then released, and ends when promoter clearance takes place.

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 0.501
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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • GO:1903865 A protein complex which is capable of sigma factor antagonist activity.
  • GO:0003899 Catalysis of the reaction: nucleoside triphosphate + RNA(n) = diphosphate + RNA(n+1). Utilizes a DNA template, i.e. the catalysis of DNA-template-directed extension of the 3'-end of an RNA strand by one nucleotide at a time. Can initiate a chain 'de novo'.
  • GO:0016987 Sigma factors act as the promoter specificity subunit of eubacterial and plant plastid multisubunit RNA polymerases, whose core subunit composition is often described as alpha(2)-beta-beta-prime. Although sigma does not bind DNA on its own, when combined with the core to form the holoenzyme, the sigma factor binds specifically to promoter elements. The sigma subunit is released once elongation begins.
  • GO:0000976 Binding to a specific sequence of DNA that is part of a regulatory region that controls transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.
  • GO:0006352 The initial step of transcription, consisting of the assembly of the RNA polymerase preinitiation complex (PIC) at a gene promoter, as well as the formation of the first few bonds of the RNA transcript. Transcription initiation includes abortive initiation events, which occur when the first few nucleotides are repeatedly synthesized and then released, and ends when promoter clearance takes place.
  • GO:0006355 Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • 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.

Sequence Features

Domain/signature hits from InterPro and related databases.

54 records
Show feature table
Start End DB Term Name
6 83 Pfam PF03979 Sigma-70 factor, region 1.1
6 83 InterPro IPR007127 RNA polymerase sigma factor 70, region 1.1
113 452 Gene3D G3DSA:1.10.601.10 RNA Polymerase Primary Sigma Factor
456 532 Gene3D G3DSA:1.10.10.10 -
456 532 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
551 604 Pfam PF04545 Sigma-70, region 4
551 604 InterPro IPR007630 RNA polymerase sigma-70 region 4
407 420 ProSitePatterns PS00715 Sigma-70 factors family signature 1.
407 420 InterPro IPR000943 RNA polymerase sigma-70
383 452 Pfam PF04542 Sigma-70 region 2
383 452 InterPro IPR007627 RNA polymerase sigma-70 region 2
6 616 Hamap MF_00963 RNA polymerase sigma factor RpoD [rpoD].
6 616 InterPro IPR028630 RNA polymerase sigma factor RpoD
139 352 Pfam PF04546 Sigma-70, non-essential region
139 352 InterPro IPR007631 RNA polymerase sigma factor 70, non-essential domain
115 450 SUPERFAMILY SSF88946 Sigma2 domain of RNA polymerase sigma factors
115 450 InterPro IPR013325 RNA polymerase sigma factor, region 2
545 603 CDD cd06171 Sigma70_r4
4 66 Gene3D G3DSA:1.10.220.120 -
4 66 InterPro IPR042189 Sigma-70 factor, region 1.1 superfamily
462 538 Pfam PF04539 Sigma-70 region 3
462 538 InterPro IPR007624 RNA polymerase sigma-70 region 3
513 615 SUPERFAMILY SSF88659 Sigma3 and sigma4 domains of RNA polymerase sigma factors
513 615 InterPro IPR013324 RNA polymerase sigma factor, region 3/4-like
98 128 Pfam PF00140 Sigma-70 factor, region 1.2
98 128 InterPro IPR009042 RNA polymerase sigma-70 region 1.2
4 66 FunFam G3DSA:1.10.220.120:FF:000001 RNA polymerase sigma factor RpoD
379 615 NCBIfam TIGR02393 RNA polymerase sigma factor RpoD
379 615 InterPro IPR012760 RNA polymerase sigma factor RpoD, C-terminal
334 382 Coils Coil Coil
533 616 FunFam G3DSA:1.10.10.10:FF:000004 RNA polymerase sigma factor SigA
113 452 FunFam G3DSA:1.10.601.10:FF:000002 RNA polymerase sigma factor RpoD
193 216 MobiDBLite mobidb-lite consensus disorder prediction
577 597 Coils Coil Coil
576 591 PRINTS PR00046 Major sigma-70 factor signature
576 591 InterPro IPR000943 RNA polymerase sigma-70
591 602 PRINTS PR00046 Major sigma-70 factor signature
591 602 InterPro IPR000943 RNA polymerase sigma-70
407 420 PRINTS PR00046 Major sigma-70 factor signature
431 439 PRINTS PR00046 Major sigma-70 factor signature
431 439 InterPro IPR000943 RNA polymerase sigma-70
555 567 PRINTS PR00046 Major sigma-70 factor signature
555 567 InterPro IPR000943 RNA polymerase sigma-70
11 615 PANTHER PTHR30603 RNA POLYMERASE SIGMA FACTOR RPO
456 529 SUPERFAMILY SSF88659 Sigma3 and sigma4 domains of RNA polymerase sigma factors
456 529 InterPro IPR013324 RNA polymerase sigma factor, region 3/4-like
379 604 NCBIfam TIGR02937 sigma-70 family RNA polymerase sigma factor
379 604 InterPro IPR014284 RNA polymerase sigma-70 like domain
456 532 FunFam G3DSA:1.10.10.10:FF:000002 RNA polymerase sigma factor SigA
533 617 Gene3D G3DSA:1.10.10.10 -
533 617 InterPro IPR036388 Winged helix-like DNA-binding domain superfamily
170 227 MobiDBLite mobidb-lite consensus disorder prediction
576 602 ProSitePatterns PS00716 Sigma-70 factors family signature 2.
576 602 InterPro IPR000943 RNA polymerase sigma-70

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

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold PA0576
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
2 0.454

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.

62 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
118 P00579 430.2 Da LogP 3.06 TPSA 0.0 ✓ Ro5 ✓ Clean c1ccc(cc1)[Sb+](c2ccccc2)(c3ccccc3)c4ccccc4
1N7 P00579 631.9 Da LogP 2.20 TPSA 164.4 2 viol. ✓ Clean C[C@H](CCC(=O)NCCC[N+](C)(C)CC(CS(=O)(=O)O)O)[C…
1RL P00579 900.0 Da LogP 6.67 TPSA 216.4 3 viol. ✓ Clean CCN(CC)CCOc1cccc2c1N=C3c4c5c(c(c6c4C(=O)[C@](O6…
1RM P00579 1035.2 Da LogP 6.62 TPSA 237.5 3 viol. ✓ Clean Cc1c(c2c3c4c1O[C@@](C4=O)(O/C=C/[C@@H]([C@H]([C…
88G P9WGI1 358.4 Da LogP 3.97 TPSA 58.2 ✓ Ro5 ✓ Clean Cc1ccccc1NC(=O)[C@@H](Cc2ccccc2)NC(=O)c3ccccc3
BU3 A0A0H3CAV3 90.1 Da LogP -0.25 TPSA 40.5 ✓ Ro5 ✓ Clean C[C@H]([C@@H](C)O)O
FI8 P9WGI1 1058.1 Da LogP 6.23 TPSA 266.7 4 viol. ✓ Clean CCc1c(c(c(c(c1Cl)O)Cl)O)C(=O)O[C@@H]2[C@H](O[C@…
KNG A0QW02 986.1 Da LogP 5.64 TPSA 292.6 4 viol. Alert Cc1c(c2c3c(cc(c2O)NC(=O)/C(=C\CC[C@@H]([C@@H]([…
RBT Q5SKW1 847.0 Da LogP 4.62 TPSA 205.5 2 viol. Alert Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C…
RFP A0QW02 823.0 Da LogP 4.34 TPSA 220.1 3 viol. Alert Cc1c(c2c3c4c1O[C@@](C4=O)(O\C=C\[C@@H]([C@H]([C…
RFV Q5SKW1 699.8 Da LogP 4.60 TPSA 204.5 3 viol. ✓ Clean Cc1c(c2c3c(cc(c2O)NC(=O)C(=C/C=C/[C@@H]([C@@H](…
SRN A0QW02 807.0 Da LogP 6.80 TPSA 161.2 2 viol. ✓ Clean C[C@H]1[C@H]2C\C=C\[C@H]3[C@@H]([C@H]4C[C@@H](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.