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DNA_topoisomerase_II

Euk-Vir

Only_Syngen_Nebraska_virus_5

DNA_topoisomerase_II__YP_009325819__Only_Syngen_Nebraska_virus_5__1917232

Identity

Accession:
YP_009325819 ↗
Protein ID:
DNA_topoisomerase_II
Kingdom:
euk

Quality

91.1 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Megaviricetes› Algavirales› Phycodnaviridae› Chlorovirus› Only_Syngen_Nebraska_virus_5

TaxID: 1917232

Cluster

View cluster (39 members)

3D Structure

Download PDB Download Scores JSON

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 240-374
PDB
Domain cluster: rep: DNA_gyrase_subunit_B__YP_009352802__Kaumoebavirus_Viruses.__X__D311-415
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00204.32 best DNA_gyraseB 73.4 2.30e-20 98.5% 70.7%
D2 high residues 386-527_565-640
PDB
Domain cluster: rep: DNA_topoisomerase_2__YP_009162467__Salmon_gill_poxvirus__1680908__D385-517_553-621_640-664
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF01751.29 best Toprim 38.2 1.80e-09 53.7% 84.4%
PF16898.11 TOPRIM_C 72.4 5.50e-20 38.5% 60.2%
D3 high residues 836-919
PDB
Domain cluster: rep: IMGVR_UViG_3300007985_000017-3300007985-Ga0100381_100027569__D212-299
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00521.27 best DNA_topoisoIV 32.8 5.20e-08 97.6% 12.8%
D4 high residues 948-1060
PDB
Domain cluster: rep: MH494197.1__AXC39168.1__X__00456__D116-252
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00521.27 best DNA_topoisoIV 47.7 1.50e-12 99.1% 26.7%
D5 medium residues 49-66_96-143
PDB
Domain cluster: rep: hypothetical_protein_MIV086L__YP_654658__Invertebrate_iridescent_virus_3__345201__D114-178
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1pvgA01 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.99 95.0 6.12e-01 100.0% 39.8%
ECOD (7)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3789605 225.1.1.0 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 0.99 96.0 6.14e-01 100.0% 39.6%
3998214 225.1.1.3 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.99 95.0 6.07e-01 100.0% 38.0%
3594649 225.1.1.0 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 0.96 92.0 5.95e-01 100.0% 40.4%
4617838 225.1.1.3 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.96 92.0 5.93e-01 100.0% 40.4%
3883105 3226.1.1.1 ↗ alpha complex topology › Uracil Transporter UraA › Uracil Transporter UraA › Uracil Transporter UraA › Xan_ur_permease 0.56 48.0 2.88e-01 100.0% 75.6%
4021456 633.1.1.0 ↗ alpha bundles › Bromodomain-like › Bromodomain › Bromodomain 0.52 40.0 3.43e-01 87.9% 84.3%
3364871 3711.1.1.4 ↗ alpha bundles › LTXXQ motif family protein › LTXXQ motif family protein › LTXXQ motif family protein › DOG1 0.50 43.0 3.03e-01 100.0% 92.4%
D6 medium residues 67-95_144-239
PDB
Domain cluster: rep: SR-VP_2-4_scaffold_141_2548329_prodigal-single.1__X__X__00037__D32-204
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1pvgA01 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.97 95.0 7.26e-01 100.0% 73.4%
1s14B00 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.84 76.0 6.62e-01 94.4% 83.7%
1aj6A00 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.82 73.0 6.14e-01 92.8% 79.4%
1wh0A01 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.65 34.0 3.68e-01 80.8% 57.7%
4feiA00 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.61 30.0 3.36e-01 80.8% 57.8%
3h6eB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.54 37.0 4.06e-01 97.6% 87.9%
3w1zC00 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.54 30.0 2.99e-01 80.8% 51.5%
6ewnA00 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 29.0 3.20e-01 80.8% 66.7%
3nuwA01 3.30.420.300 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 2-keto-3-deoxy-galactonokinase, substrate binding domain 0.52 34.0 3.89e-01 90.4% 91.1%
2qi2A02 3.30.420.60 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 0.51 33.0 3.45e-01 95.2% 70.2%
3agkA02 3.30.420.60 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 0.51 37.0 3.81e-01 89.6% 77.4%
3hrgA02 3.30.420.260 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Protein of unknown function DUF3822, C-terminal domain 0.51 33.0 3.42e-01 91.2% 70.2%
2vsmA00 2.120.10.10 Mainly Beta › 6 Propeller › Neuraminidase › 0.51 41.0 2.92e-01 88.0% 93.5%
3cj1A02 3.30.420.150 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Exopolyphosphatase. Domain 2 0.50 41.0 3.20e-01 86.4% 86.7%
3qeeB00 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.50 40.0 3.09e-01 86.4% 70.9%
ECOD (23)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3789605 225.1.1.0 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 0.98 89.0 6.77e-01 92.8% 69.8%
4617838 225.1.1.3 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.97 89.0 6.83e-01 94.4% 71.4%
3594649 225.1.1.0 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 0.97 89.0 6.82e-01 94.4% 71.4%
3998214 225.1.1.3 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.96 94.0 7.09e-01 100.0% 69.8%
4875911 225.1.1.3 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.93 90.0 6.76e-01 100.0% 72.0%
3198261 225.1.1.0 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 0.83 76.0 6.40e-01 94.4% 93.2%
3413099 319.1.1.3 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › CS 0.70 31.0 3.52e-01 80.8% 53.0%
5001498 319.1.1.4 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › ArsA_HSP20 0.70 29.0 3.04e-01 80.8% 40.8%
5074343 319.1.1.23 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › PF29697 0.69 29.0 3.72e-01 80.8% 65.3%
5004113 319.1.1.0 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones 0.68 29.0 3.67e-01 80.8% 65.3%
5027182 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.61 33.0 3.49e-01 80.8% 59.1%
3509551 319.1.1.0 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones 0.59 28.0 3.32e-01 77.6% 64.7%
3464766 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.59 31.0 3.06e-01 83.2% 47.4%
3239567 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.59 29.0 3.18e-01 80.8% 56.2%
5076783 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.59 30.0 3.26e-01 80.8% 58.1%
5054294 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.58 30.0 3.35e-01 80.8% 62.0%
5051062 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.58 29.0 3.25e-01 80.8% 60.2%
3500564 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.57 30.0 3.30e-01 84.8% 60.0%
4964479 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.56 30.0 3.16e-01 80.8% 56.5%
3739716 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.56 30.0 3.20e-01 80.8% 57.4%
4008223 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.55 28.0 2.99e-01 80.8% 55.5%
3509197 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.52 27.0 3.18e-01 77.6% 70.6%
3323077 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.52 30.0 3.30e-01 80.8% 68.6%
D7 medium residues 531-563
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF16898.11 best TOPRIM_C 30.0 7.60e-07 100.0% 24.2%
D8 medium residues 641-774
PDB
Domain cluster: rep: DNA_topoisomerase_2__YP_009162467__Salmon_gill_poxvirus__1680908__D669-796
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00521.27 best DNA_topoisoIV 164.1 7.30e-48 92.5% 28.3%
D9 medium residues 775-833_920-935
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00521.27 best DNA_topoisoIV 83.6 1.90e-23 100.0% 15.6%
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1bjtA05 3.90.199.10 Alpha Beta › Alpha-Beta Complex › Topoisomerase II; domain 5 › Topoisomerase II, domain 5 0.99 93.0 6.10e-01 100.0% 28.9%
4bu0A01 3.40.50.10190 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › BRCT domain 0.55 38.0 3.51e-01 72.0% 78.6%
ECOD (20)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3719735 4014.1.1.1 ↗ a+b two layers › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › DNA_topoisoIV 1.00 86.0 6.29e-01 88.0% 98.2%
3188905 4014.1.1.1 ↗ a+b two layers › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › DNA_topoisoIV 0.98 84.0 6.02e-01 88.0% 98.3%
3998667 4014.1.1.1 ↗ a+b two layers › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › DNA_topoisoIV 0.98 86.0 6.03e-01 90.7% 88.2%
3789606 4014.1.1.0 ↗ a+b two layers › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase 0.97 86.0 6.32e-01 92.0% 100.0%
3220665 4014.1.1.1 ↗ a+b two layers › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › DNA_topoisoIV 0.97 86.0 6.22e-01 92.0% 99.4%
3277529 4014.1.1.1 ↗ a+b two layers › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › DNA_topoisoIV 0.96 79.0 5.90e-01 85.3% 100.0%
2390536 4014.1.1.1 ↗ a+b two layers › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › DNA_topoisoIV 0.95 75.0 5.58e-01 81.3% 43.2%
3594650 4014.1.1.0 ↗ a+b two layers › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase 0.94 77.0 5.79e-01 85.3% 100.0%
3614277 4014.1.1.1 ↗ a+b two layers › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › DNA_topoisoIV 0.94 80.0 5.81e-01 89.3% 90.6%
4024263 4014.1.1.1 ↗ a+b two layers › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › DNA_topoisoIV 0.91 79.0 5.49e-01 92.0% 99.5%
3965475 4014.1.1.1 ↗ a+b two layers › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › DNA_topoisoIV 0.90 78.0 5.48e-01 90.7% 100.0%
3962339 4014.1.1.0 ↗ a+b two layers › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase 0.89 74.0 5.31e-01 86.7% 100.0%
4946212 4014.1.1.1 ↗ a+b two layers › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › DNA_topoisoIV 0.88 73.0 5.29e-01 86.7% 100.0%
396210 4014.1.1.1 ↗ a+b two layers › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › DNA_topoisoIV 0.88 82.0 5.55e-01 98.7% 80.8%
3590557 4014.1.1.1 ↗ a+b two layers › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › DNA_topoisoIV 0.88 76.0 5.42e-01 90.7% 93.8%
4624017 4014.1.1.1 ↗ a+b two layers › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › DNA_topoisoIV 0.88 75.0 5.53e-01 90.7% 100.0%
4266765 4014.1.1.1 ↗ a+b two layers › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › DNA_topoisoIV 0.88 76.0 5.73e-01 92.0% 100.0%
3096551 4014.1.1.1 ↗ a+b two layers › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › DNA_topoisoIV 0.83 68.0 5.03e-01 88.0% 99.5%
2140592 4014.1.1.1 ↗ a+b two layers › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › a+b domain in type II DNA topoisomerase › DNA_topoisoIV 0.82 71.0 5.15e-01 90.7% 100.0%
3599809 3279.1.1.0 ↗ alpha arrays › Helical domain in 5'->3' exoribonucleases › Helical domain in 5'->3' exoribonucleases › Helical domain in 5'->3' exoribonucleases 0.51 40.0 2.89e-01 92.0% 49.6%