Protein profile

KP13_02791

DNA topoisomerase 4 subunit B

Genome: KpKP13

Gene: parE AHE42640.1 Structure source: AlphaFold + ColabFold UniProt A0A0H3H365
Amino acids 631
Annotations 5
Features 75
PDB binders 20
Druggability 0.795

Overview

Basic information about this protein and its source genome.

Accession
KP13_02791
Gene
parE AHE42640.1
Status
annotated
Amino acids
631
Structure source
AlphaFold + ColabFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
24.696
Human E-value
4.83e-31
Gut microbiome off-target
hit
Essential (DEG)
Y
DEG identity (%)
94.929
DEG E-value
0.0
Localization
Cytoplasmic
ColabFold pLDDT
87.97

Selected Druggability evidence

AlphaFold / UniProt model

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 0.795
Structure A0A0H3H365
Pocket Pocket 3
P2Rank 0.816
Structure A0A0H3H365
Pocket Pocket 1
ColabFold model
FPocket 0.927 · Pocket 1
P2Rank 0.891 · Pocket 1
Core conservation Conserved core gene
Roary core
CoreCruncher core
Gut microbiome 194 / 4744 genomes with a hit
Normalized 0.041

Sequence

Primary amino-acid sequence viewer.

Functional Annotations

Enzyme classification and Gene Ontology terms linked to this protein.

5 GO

Gene Ontology (GO)

5
  • 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.
  • GO:0005524 Binding to ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
  • GO:0005694 A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
  • 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:0003677 Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).

Sequence Features

Domain/signature hits from InterPro and related databases.

75 records
Show feature table
Start End DB Term Name
217 390 Gene3D G3DSA:3.30.230.10 -
217 390 InterPro IPR014721 Ribosomal protein S5 domain 2-type fold, subgroup
28 174 SMART SM00387 HKATPase_4
28 174 InterPro IPR003594 Histidine kinase/HSP90-like ATPase
389 622 SUPERFAMILY SSF56719 Type II DNA topoisomerase
389 622 InterPro IPR013760 DNA topoisomerase, type IIA-like domain superfamily
35 625 SMART SM00433 topII5
35 625 InterPro IPR001241 DNA topoisomerase, type IIA
217 390 FunFam G3DSA:3.30.230.10:FF:000012 DNA topoisomerase 4 subunit B
5 626 NCBIfam TIGR01055 DNA topoisomerase IV subunit B
5 626 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
414 522 Pfam PF01751 Toprim domain
414 522 InterPro IPR006171 TOPRIM domain
3 216 Gene3D G3DSA:3.30.565.10 -
3 216 InterPro IPR036890 Histidine kinase/HSP90-like ATPase superfamily
413 526 ProSiteProfiles PS50880 Toprim domain profile.
413 526 InterPro IPR006171 TOPRIM domain
3 629 Hamap MF_00938 DNA topoisomerase 4 subunit B [parE].
3 629 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
218 383 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like
218 383 InterPro IPR020568 Ribosomal protein S5 domain 2-type fold
6 216 SUPERFAMILY SSF55874 ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
6 216 InterPro IPR036890 Histidine kinase/HSP90-like ATPase superfamily
2 629 PANTHER PTHR45866 DNA GYRASE/TOPOISOMERASE SUBUNIT B
33 214 CDD cd16928 HATPase_GyrB-like
417 425 ProSitePatterns PS00177 DNA topoisomerase II signature.
417 425 InterPro IPR018522 DNA topoisomerase, type IIA, conserved site
557 621 Pfam PF00986 DNA gyrase B subunit, carboxyl terminus
557 621 InterPro IPR002288 DNA gyrase B subunit, C-terminal
29 172 Pfam PF02518 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
29 172 InterPro IPR003594 Histidine kinase/HSP90-like ATPase
391 624 FunFam G3DSA:3.40.50.670:FF:000003 DNA topoisomerase 4 subunit B
175 192 PRINTS PR01098 Topoisomerase IV subunit B signature
175 192 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
193 214 PRINTS PR01098 Topoisomerase IV subunit B signature
193 214 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
312 327 PRINTS PR01098 Topoisomerase IV subunit B signature
312 327 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
150 165 PRINTS PR01098 Topoisomerase IV subunit B signature
150 165 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
504 520 PRINTS PR01098 Topoisomerase IV subunit B signature
504 520 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
470 482 PRINTS PR01098 Topoisomerase IV subunit B signature
470 482 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
136 150 PRINTS PR01098 Topoisomerase IV subunit B signature
136 150 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
239 262 PRINTS PR01098 Topoisomerase IV subunit B signature
239 262 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
449 470 PRINTS PR01098 Topoisomerase IV subunit B signature
449 470 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
27 40 PRINTS PR01098 Topoisomerase IV subunit B signature
27 40 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
295 311 PRINTS PR01098 Topoisomerase IV subunit B signature
295 311 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
538 560 PRINTS PR01098 Topoisomerase IV subunit B signature
538 560 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
339 362 PRINTS PR01098 Topoisomerase IV subunit B signature
339 362 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
363 388 PRINTS PR01098 Topoisomerase IV subunit B signature
363 388 InterPro IPR005737 DNA topoisomerase IV, subunit B, Gram-negative
391 624 Gene3D G3DSA:3.40.50.670 -
391 624 InterPro IPR013759 DNA topoisomerase, type IIA, subunit B, C-terminal
498 515 PRINTS PR00418 DNA topoisomerase II family signature
110 124 PRINTS PR00418 DNA topoisomerase II family signature
67 80 PRINTS PR00418 DNA topoisomerase II family signature
267 280 PRINTS PR00418 DNA topoisomerase II family signature
480 496 PRINTS PR00418 DNA topoisomerase II family signature
32 47 PRINTS PR00418 DNA topoisomerase II family signature
518 530 PRINTS PR00418 DNA topoisomerase II family signature
561 577 PRINTS PR00418 DNA topoisomerase II family signature
415 429 PRINTS PR00418 DNA topoisomerase II family signature
219 385 Pfam PF00204 DNA gyrase B
219 385 InterPro IPR013506 DNA topoisomerase, type IIA, subunit B, domain 2
3 217 FunFam G3DSA:3.30.565.10:FF:000002 DNA gyrase subunit B
218 387 CDD cd00822 TopoII_Trans_DNA_gyrase

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

0 + 2

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

Entry Method Resolution Chain Coverage Links Status
AlphaFold AF_A0A0H3H365
AlphaFold full sequence Viewing
ColabFold KP13_02791
ColabFold 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
3 0.795
44 0.317

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 12.85 0.664
2 3.04 0.101
3 1.66 0.028
4 1.15 0.009

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.

88 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
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
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
1UV Q59961 373.4 Da LogP 1.61 TPSA 97.8 ✓ Ro5 ✓ Clean c1c2c(c3c(c1F)N4CC[C@H]([C@H]4COC3)N)N(C=C(C2=O…
1YP Q8DQB5 477.4 Da LogP 3.77 TPSA 138.7 ✓ Ro5 ✓ Clean CCNC(=O)Nc1cc(c(cn1)c2cc(cnc2)C3=NNC(=O)O3)c4nc…
2B7 Q8DQB5 397.5 Da LogP 3.87 TPSA 88.9 ✓ Ro5 ✓ Clean CC(C)CCN1c2c(nc(s2)NC(=O)NCC=C)C=C(C1=O)c3cccnc3
AF5 Q59961 369.4 Da LogP 2.50 TPSA 88.6 ✓ Ro5 ✓ Clean c1c2c(c3c(c1F)N4CC[C@H]([C@H]4CC=C3)N)N(C=C(C2=…
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 A0A0J9WZF0 442.9 Da LogP 2.49 TPSA 129.5 ✓ Ro5 ✓ Clean CCc1c(c2c([nH]1)nc(nc2N3CC[C@H](C3)N)Sc4cc5c(nc…
DOO A0A0J9WZF0 434.5 Da LogP 2.98 TPSA 103.9 ✓ Ro5 ✓ Clean Cc1ncc(cn1)Oc2nc3c(c4cc(cc(c4[nH]3)NC)F)c(n2)N5…
LFX Q59961 361.4 Da LogP 1.54 TPSA 75.0 ✓ Ro5 ✓ Clean C[C@H]1COc2c3c(cc(c2N4CCN(CC4)C)F)C(=O)C(=CN31)…
MFX Q59961 401.4 Da LogP 2.37 TPSA 83.8 ✓ Ro5 ✓ Clean COc1c2c(cc(c1N3C[C@@H]4CCCN[C@@H]4C3)F)C(=O)C(=…
NFX Q59961 365.8 Da LogP 2.36 TPSA 88.6 ✓ Ro5 ✓ Clean c1c2c(c(c(c1F)N3CC[C@H](C3)N)Cl)N(C=C(C2=O)C(=O…
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…
PDQ Q59961 361.4 Da LogP 0.83 TPSA 99.3 ✓ Ro5 ✓ Clean Cc1c2c(cc(c1N3CC[C@H](C3)[C@H](C)N)F)C(=O)N(C(=…
TR6 Q59961 416.4 Da LogP 1.89 TPSA 101.5 ✓ Ro5 ✓ Clean c1cc(c(cc1F)F)N2C=C(C(=O)c3c2nc(c(c3)F)N4C[C@@H…
TSJ Q8DQB5 403.4 Da LogP 4.66 TPSA 95.1 ✓ Ro5 ✓ Clean Cc1cc(cc(c1)C(F)(F)F)c2cc([nH]n2)NC(=O)c3ccc(cc…
TTJ Q8DQB5 301.3 Da LogP 2.05 TPSA 76.2 ✓ Ro5 ✓ Clean Cc1cc(cc(c1)c2cc([nH]n2)NC(=O)[C@H]3COCCO3)C

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.