Protein profile

PA0004

DNA gyrase subunit B

Genome: NC_002516.2

Gene: PA0004 gyrB Structure source: Experimental + AlphaFold UniProt Q9I7C2
Amino acids 806
Annotations 9
Features 78
PDB binders 70
Druggability 0.61

Overview

Basic information about this protein and its source genome.

Accession
PA0004
Gene
PA0004 gyrB
Status
annotated
Amino acids
806
Structure source
Experimental + AlphaFold

Target profile

Computed evidence for target prioritization.

Human off-target
hit
Human identity (%)
23.951
Human E-value
2.9700000000000003e-31
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 0.61
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:0005737 The contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  • 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: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:0006261 A DNA replication process that uses parental DNA as a template for the DNA-dependent DNA polymerases that synthesize the new strands.

Sequence Features

Domain/signature hits from InterPro and related databases.

78 records
Show feature table
Start End DB Term Name
393 593 FunFam G3DSA:3.40.50.670:FF:000005 DNA gyrase subunit B
72 85 PRINTS PR00418 DNA topoisomerase II family signature
489 505 PRINTS PR00418 DNA topoisomerase II family signature
527 539 PRINTS PR00418 DNA topoisomerase II family signature
115 129 PRINTS PR00418 DNA topoisomerase II family signature
270 283 PRINTS PR00418 DNA topoisomerase II family signature
738 754 PRINTS PR00418 DNA topoisomerase II family signature
422 436 PRINTS PR00418 DNA topoisomerase II family signature
37 52 PRINTS PR00418 DNA topoisomerase II family signature
507 524 PRINTS PR00418 DNA topoisomerase II family signature
399 591 Gene3D G3DSA:3.40.50.670 -
399 591 InterPro IPR013759 DNA topoisomerase, type IIA, subunit B, C-terminal
221 379 CDD cd00822 TopoII_Trans_DNA_gyrase
222 398 Gene3D G3DSA:3.30.230.10 -
222 398 InterPro IPR014721 Ribosomal protein S5 domain 2-type fold, subgroup
424 432 ProSitePatterns PS00177 DNA topoisomerase II signature.
424 432 InterPro IPR018522 DNA topoisomerase, type IIA, conserved site
566 732 Pfam PF18053 DNA gyrase B subunit insert domain
566 732 InterPro IPR041423 DNA gyrase subunit B insert domain
38 217 CDD cd16928 HATPase_GyrB-like
3 805 PANTHER PTHR45866 DNA GYRASE/TOPOISOMERASE SUBUNIT B
33 177 SMART SM00387 HKATPase_4
33 177 InterPro IPR003594 Histidine kinase/HSP90-like ATPase
420 534 CDD cd03366 TOPRIM_TopoIIA_GyrB
420 534 InterPro IPR034160 DNA gyrase subunit B, TOPRIM domain
37 799 SMART SM00433 topII5
37 799 InterPro IPR001241 DNA topoisomerase, type IIA
4 806 Hamap MF_01898 DNA gyrase subunit B [gyrB].
4 806 InterPro IPR011557 DNA gyrase, subunit B
34 176 Pfam PF02518 Histidine kinase-, DNA gyrase B-, and HSP90-like ATPase
34 176 InterPro IPR003594 Histidine kinase/HSP90-like ATPase
7 219 SUPERFAMILY SSF55874 ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
7 219 InterPro IPR036890 Histidine kinase/HSP90-like ATPase superfamily
4 220 FunFam G3DSA:3.30.565.10:FF:000002 DNA gyrase subunit B
705 806 Gene3D G3DSA:3.40.50.670 -
705 806 InterPro IPR013759 DNA topoisomerase, type IIA, subunit B, C-terminal
595 684 Gene3D G3DSA:3.10.20.690 -
221 394 FunFam G3DSA:3.30.230.10:FF:000005 DNA gyrase subunit B
222 394 SUPERFAMILY SSF54211 Ribosomal protein S5 domain 2-like
222 394 InterPro IPR020568 Ribosomal protein S5 domain 2-type fold
222 392 Pfam PF00204 DNA gyrase B
222 392 InterPro IPR013506 DNA topoisomerase, type IIA, subunit B, domain 2
595 684 FunFam G3DSA:3.10.20.690:FF:000002 DNA gyrase subunit B
7 806 NCBIfam TIGR01059 DNA gyrase subunit B
7 806 InterPro IPR011557 DNA gyrase, subunit B
314 330 PRINTS PR01159 DNA gyrase subunit B signature
314 330 InterPro IPR000565 DNA topoisomerase, type IIA, subunit B
197 210 PRINTS PR01159 DNA gyrase subunit B signature
197 210 InterPro IPR000565 DNA topoisomerase, type IIA, subunit B
221 243 PRINTS PR01159 DNA gyrase subunit B signature
221 243 InterPro IPR000565 DNA topoisomerase, type IIA, subunit B
182 197 PRINTS PR01159 DNA gyrase subunit B signature
182 197 InterPro IPR000565 DNA topoisomerase, type IIA, subunit B
362 376 PRINTS PR01159 DNA gyrase subunit B signature
362 376 InterPro IPR000565 DNA topoisomerase, type IIA, subunit B
759 771 PRINTS PR01159 DNA gyrase subunit B signature
759 771 InterPro IPR000565 DNA topoisomerase, type IIA, subunit B
775 791 PRINTS PR01159 DNA gyrase subunit B signature
775 791 InterPro IPR000565 DNA topoisomerase, type IIA, subunit B
244 262 PRINTS PR01159 DNA gyrase subunit B signature
244 262 InterPro IPR000565 DNA topoisomerase, type IIA, subunit B
376 396 PRINTS PR01159 DNA gyrase subunit B signature
376 396 InterPro IPR000565 DNA topoisomerase, type IIA, subunit B
7 17 PRINTS PR01159 DNA gyrase subunit B signature
7 17 InterPro IPR000565 DNA topoisomerase, type IIA, subunit B
472 481 PRINTS PR01159 DNA gyrase subunit B signature
472 481 InterPro IPR000565 DNA topoisomerase, type IIA, subunit B
706 805 FunFam G3DSA:3.40.50.670:FF:000004 DNA gyrase subunit B
396 796 SUPERFAMILY SSF56719 Type II DNA topoisomerase
396 796 InterPro IPR013760 DNA topoisomerase, type IIA-like domain superfamily
421 533 Pfam PF01751 Toprim domain
421 533 InterPro IPR006171 TOPRIM domain
4 221 Gene3D G3DSA:3.30.565.10 -
4 221 InterPro IPR036890 Histidine kinase/HSP90-like ATPase superfamily
420 535 ProSiteProfiles PS50880 Toprim domain profile.
420 535 InterPro IPR006171 TOPRIM domain
734 795 Pfam PF00986 DNA gyrase B subunit, carboxyl terminus
734 795 InterPro IPR002288 DNA gyrase B subunit, C-terminal

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

5 + 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 7PTF
X-ray 1.32 Å A,B,C
27.4% 1-221
Viewing
PDB 8BN6
X-ray 1.60 Å A
27.4% 1-221
Loaded
PDB 6M1J
X-ray 1.70 Å A,B
25.4% 17-221
Loaded
PDB 7PTG
X-ray 2.20 Å A,B
27.4% 1-221
Loaded
PDB 6M1S
X-ray 2.25 Å A,B
25.4% 17-221
Loaded
AlphaFold PA0004
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
2 0.61
3 0.545
1 0.485

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 10.69 0.574
2 4.37 0.183
3 2.62 0.076
4 1.91 0.039

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.

220 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.

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Ligand Source crystal MW · LogP · TPSA Lipinski PAINS SMILES
EZ6 511.4 Da LogP 4.67 TPSA 121.6 1 viol. ✓ Clean CNc1cc(cc2c1[nH]c3c2c(c(cn3)c4cnc(nc4)C5(CC5)C(…
EZ9 557.5 Da LogP 5.44 TPSA 130.8 2 viol. ✓ Clean CCNc1cc(cc2c1[nH]c3c2c(c(cn3)c4cnc(nc4)OCC(C)(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.