Protein profile

PA4967

DNA topoisomerase IV subunit B

Genome: NC_002516.2

Gene: PA4967 parE Structure source: AlphaFold UniProt Q9HUJ8
Amino acids 629
Annotations 9
Features 77
PDB binders 16
Druggability 0.6

Overview

Basic information about this protein and its source genome.

Accession
PA4967
Gene
PA4967 parE
Status
annotated
Amino acids
629
Structure source
AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
25.383
Human E-value
2.4e-32
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 0.6
Structure
Pocket

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

1 EC 8 GO

Enzyme Commission (EC)

1

Gene Ontology (GO)

8
  • GO:0005694 A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
  • GO:0009340 A heterodimeric enzyme, which in most bacterial species is composed of two subunits, ParC and ParE. Functions in chromosome segregation and can relax supercoiled DNA.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
  • GO:0003918 Catalysis of a DNA topological transformation by transiently cleaving a pair of complementary DNA strands to form a gate through which a second double-stranded DNA segment is passed, after which the severed strands in the first DNA segment are rejoined, driven by ATP hydrolysis. The enzyme changes the linking number in multiples of 2.
  • GO:0046872 Binding to a metal ion.
  • GO:0007059 The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets. In eukaryotes, chromosome segregation begins with the condensation of chromosomes, includes chromosome separation, and ends when chromosomes have completed movement to the spindle poles.
  • GO:0006265 The process in which a transformation is induced in the topological structure of a double-stranded DNA helix, resulting in a change in linking number.

Sequence Features

Domain/signature hits from InterPro and related databases.

77 records
Show feature table
Start End DB Term Name
1 627 Hamap MF_00938 DNA topoisomerase 4 subunit B [parE].
1 627 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
216 386 CDD cd00822 TopoII_Trans_DNA_gyrase
31 212 CDD cd16928 HATPase_GyrB-like
191 212 PRINTS PR01098 Topoisomerase IV subunit B signature
191 212 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
148 163 PRINTS PR01098 Topoisomerase IV subunit B signature
148 163 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
310 325 PRINTS PR01098 Topoisomerase IV subunit B signature
310 325 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
134 148 PRINTS PR01098 Topoisomerase IV subunit B signature
134 148 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
361 386 PRINTS PR01098 Topoisomerase IV subunit B signature
361 386 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
447 468 PRINTS PR01098 Topoisomerase IV subunit B signature
447 468 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
536 558 PRINTS PR01098 Topoisomerase IV subunit B signature
536 558 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
337 360 PRINTS PR01098 Topoisomerase IV subunit B signature
337 360 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
468 480 PRINTS PR01098 Topoisomerase IV subunit B signature
468 480 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
237 260 PRINTS PR01098 Topoisomerase IV subunit B signature
237 260 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
293 309 PRINTS PR01098 Topoisomerase IV subunit B signature
293 309 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
583 597 PRINTS PR01098 Topoisomerase IV subunit B signature
583 597 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
25 38 PRINTS PR01098 Topoisomerase IV subunit B signature
25 38 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
502 518 PRINTS PR01098 Topoisomerase IV subunit B signature
502 518 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
173 190 PRINTS PR01098 Topoisomerase IV subunit B signature
173 190 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
33 623 SMART SM00433 topII5
33 623 InterPro IPR001241 DNA topoisomerase, type IIA
389 622 FunFam G3DSA:3.40.50.670:FF:000003 DNA topoisomerase 4 subunit B
215 388 FunFam G3DSA:3.30.230.10:FF:000012 DNA topoisomerase 4 subunit B
557 619 Pfam PF00986 DNA gyrase B subunit, carboxyl terminus
557 619 InterPro IPR002288 DNA gyrase B subunit, C-terminal
415 423 ProSitePatterns PS00177 DNA topoisomerase II signature.
415 423 InterPro IPR018522 DNA topoisomerase, type IIA, conserved site
412 521 Pfam PF01751 Toprim domain
412 521 InterPro IPR006171 TOPRIM domain
1 214 Gene3D G3DSA:3.30.565.10 -
1 214 InterPro IPR036890 Histidine kinase/HSP90-like ATPase superfamily
215 388 Gene3D G3DSA:3.30.230.10 -
215 388 InterPro IPR014721 Ribosomal protein S5 domain 2-type fold, subgroup
26 172 SMART SM00387 HKATPase_4
26 172 InterPro IPR003594 Histidine kinase/HSP90-like ATPase
4 214 SUPERFAMILY SSF55874 ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
4 214 InterPro IPR036890 Histidine kinase/HSP90-like ATPase superfamily
2 623 NCBIfam TIGR01055 DNA topoisomerase IV subunit B
2 623 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
411 524 ProSiteProfiles PS50880 Toprim domain profile.
411 524 InterPro IPR006171 TOPRIM domain
216 381 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like
216 381 InterPro IPR020568 Ribosomal protein S5 domain 2-type fold
387 620 SUPERFAMILY SSF56719 Type II DNA topoisomerase
387 620 InterPro IPR013760 DNA topoisomerase, type IIA-like domain superfamily
1 215 FunFam G3DSA:3.30.565.10:FF:000002 DNA gyrase subunit B
3 624 PANTHER PTHR45866 DNA GYRASE/TOPOISOMERASE SUBUNIT B
389 622 Gene3D G3DSA:3.40.50.670 -
389 622 InterPro IPR013759 DNA topoisomerase, type IIA, subunit B, C-terminal
413 427 PRINTS PR00418 DNA topoisomerase II family signature
265 278 PRINTS PR00418 DNA topoisomerase II family signature
561 577 PRINTS PR00418 DNA topoisomerase II family signature
496 513 PRINTS PR00418 DNA topoisomerase II family signature
30 45 PRINTS PR00418 DNA topoisomerase II family signature
108 122 PRINTS PR00418 DNA topoisomerase II family signature
516 528 PRINTS PR00418 DNA topoisomerase II family signature
65 78 PRINTS PR00418 DNA topoisomerase II family signature
478 494 PRINTS PR00418 DNA topoisomerase II family signature
217 384 Pfam PF00204 DNA gyrase B
217 384 InterPro IPR013506 DNA topoisomerase, type IIA, subunit B, domain 2
27 170 Pfam PF02518 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
27 170 InterPro IPR003594 Histidine kinase/HSP90-like ATPase

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 PA4967
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 0.6
1 0.535
8 0.432

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.

84 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
0WT Q839Z1 371.8 Da LogP 2.15 TPSA 105.8 ✓ Ro5 ✓ Clean CCc1c(c2c([nH]1)nc(nc2N3C[C@@H]4[C@H](C3)C4N)Oc…
19X A0A0J9WZF0 426.9 Da LogP 3.44 TPSA 100.3 ✓ Ro5 ✓ Clean CCc1c(c2c([nH]1)nc(nc2N3CC[C@H](C3)N)Sc4ccc5c(c…
19Y A0A0J9WZF0 314.4 Da LogP 2.89 TPSA 80.8 ✓ Ro5 ✓ Clean CCc1c(c2c([nH]1)nc(nc2OC)Sc3cccnc3)C=O
1A0 Q839Z1 426.9 Da LogP 3.20 TPSA 109.5 ✓ Ro5 ✓ Clean CCc1c(c2c([nH]1)nc(nc2N3CC[C@H](C3)N)Sc4cc5c(nc…
1AV P20083 295.3 Da LogP 1.92 TPSA 95.4 ✓ Ro5 ✓ Clean c1cc(cnc1)c2nc3c(nc(nc3s2)N)n4ccnc4
1EU P20083 323.4 Da LogP 2.97 TPSA 99.8 ✓ Ro5 ✓ Clean CCNC(=O)Nc1[nH]c2cc(cc(c2n1)C(=O)C)c3cccnc3
920 Q839Z1 448.5 Da LogP 3.36 TPSA 117.9 ✓ Ro5 ✓ Clean Cc1ncc(cn1)Oc2nc3c(c4cc(cc(c4[nH]3)NC)F)c(n2)N5…
ANP P20083 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)…
BHW Q5SHZ4 1110.1 Da LogP 5.57 TPSA 354.9 4 viol. ✓ Clean Cc1ccc([nH]1)C(=O)O[C@H]2[C@H]([C@@H](OC([C@@H]…
CJC Q839Z1 442.9 Da LogP 2.49 TPSA 129.5 ✓ Ro5 ✓ Clean CCc1c(c2c([nH]1)nc(nc2N3CC[C@H](C3)N)Sc4cc5c(nc…
DOO Q839Z1 434.5 Da LogP 2.98 TPSA 103.9 ✓ Ro5 ✓ Clean Cc1ncc(cn1)Oc2nc3c(c4cc(cc(c4[nH]3)NC)F)c(n2)N5…
HTT Q839Z1 444.0 Da LogP 3.52 TPSA 107.2 ✓ Ro5 ✓ Clean CCc1c(c2c([nH]1)nc(nc2N3CC[C@H](C3)N)Sc4cc5c(nc…
MJU Q839Z1 414.5 Da LogP 3.14 TPSA 109.5 ✓ Ro5 ✓ Clean c1ccc2c(c1)c3c([nH]2)nc(nc3N4CC[C@@H](C4)N)Sc5c…
NOV P20083 612.6 Da LogP 3.63 TPSA 200.0 2 viol. ✓ Clean Cc1c(ccc2c1OC(=O)C(=C2O)NC(=O)c3ccc(c(c3)CC=C(C…
SUY Q839Z1 387.9 Da LogP 2.51 TPSA 96.6 ✓ Ro5 ✓ Clean CCc1c(c2c([nH]1)nc(nc2N3C[C@@H]4[C@H](C3)C4N)Sc…
TBU Q839Z1 74.1 Da LogP 0.78 TPSA 20.2 ✓ Ro5 ✓ Clean CC(C)(C)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.