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DNA_repair_enzyme_RAD2

Euk-Vir

European_catfish_virus

DNA_repair_enzyme_RAD2__YP_006347608__European_catfish_virus__84739

Identity

Accession:
YP_006347608 ↗
Protein ID:
DNA_repair_enzyme_RAD2
Kingdom:
euk

Quality

88.2 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Megaviricetes› Pimascovirales› Iridoviridae› Ranavirus› European_catfish_virus

TaxID: 84739

Cluster

View cluster (65 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 80-152
PDB
Domain cluster: representative
CATH (47)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3m9vA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.82 53.0 4.00e-01 100.0% 30.6%
1zpyA00 6.10.140.1960 Special › Helix non-globular › Helix Hairpins › 0.78 53.0 4.92e-01 100.0% 57.1%
3rguB00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.74 47.0 4.45e-01 100.0% 54.0%
4l0rB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.74 51.0 5.18e-01 100.0% 72.6%
4h63K00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.73 48.0 4.36e-01 100.0% 50.0%
3sjqC00 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.71 45.0 4.41e-01 94.5% 58.7%
4id0A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.71 49.0 4.26e-01 100.0% 47.3%
1k32A03 3.30.750.44 Alpha Beta › 2-Layer Sandwich › Transcription Regulator spoIIAA › 0.71 34.0 3.52e-01 98.6% 48.6%
2qffA00 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.70 40.0 4.01e-01 100.0% 54.1%
3r84B00 6.10.280.160 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Mediator of RNA polymerase II transcription subunit 22 0.69 50.0 4.83e-01 100.0% 68.8%
3nkzA00 1.20.58.380 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Flagellar protein flit. 0.68 49.0 4.53e-01 78.1% 91.8%
1xzpA02 1.20.120.430 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › tRNA modification GTPase MnmE domain 2 0.67 60.0 4.57e-01 100.0% 69.3%
6xkyA01 1.20.1330.10 Mainly Alpha › Up-down Bundle › f41 fragment of flagellin, N-terminal domain › f41 fragment of flagellin, N-terminal domain 0.67 59.0 4.41e-01 100.0% 65.8%
4v1gA00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.64 49.0 4.68e-01 100.0% 69.4%
2p5tA00 1.10.8.130 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.64 50.0 4.67e-01 98.6% 66.3%
3s84A02 1.20.120.20 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein 0.63 43.0 3.36e-01 98.6% 32.5%
3au3A00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.63 45.0 2.99e-01 75.3% 43.9%
2d2sA02 1.20.58.1220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Exo84p, C-terminal helical domain 0.63 46.0 4.16e-01 78.1% 67.3%
3axjB02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.62 40.0 3.78e-01 97.3% 55.3%
4lwsA00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.62 52.0 4.65e-01 100.0% 66.0%
2oocB00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.62 52.0 4.72e-01 98.6% 76.2%
2ccyA00 1.20.120.10 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c/b562 0.61 51.0 4.41e-01 98.6% 95.3%
2x2vA00 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.61 45.0 4.68e-01 97.3% 83.8%
1c17M00 1.20.120.220 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › ATP synthase, F0 complex, subunit A 0.60 52.0 4.25e-01 98.6% 94.4%
3ckcA02 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.60 49.0 3.82e-01 94.5% 65.5%
3favD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.60 47.0 4.64e-01 100.0% 79.5%
1bf5A01 1.20.1050.20 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › STAT transcription factor, all-alpha domain 0.59 52.0 3.93e-01 97.3% 95.2%
2oduA02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.58 52.0 4.52e-01 94.5% 86.7%
5jajA03 1.20.1320.30 Mainly Alpha › Up-down Bundle › phosphoenolpyruvate carboxylase, domain 3 › 0.58 42.0 3.64e-01 76.7% 58.6%
2yinA03 1.20.58.740 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › DOCK DHR2 domain, lobe C 0.58 47.0 3.89e-01 87.7% 92.2%
4dllB02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.58 52.0 4.25e-01 98.6% 90.8%
2xubA05 6.10.140.1450 Special › Helix non-globular › Helix Hairpins › 0.58 52.0 4.77e-01 100.0% 80.2%
1hciA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.57 51.0 4.20e-01 100.0% 56.3%
1vpdA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.57 51.0 4.23e-01 100.0% 91.6%
2i0mA01 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.57 50.0 4.38e-01 94.5% 86.8%
2fupA00 1.20.58.300 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › FlgN-like 0.57 51.0 4.21e-01 98.6% 97.6%
8gccA03 1.10.268.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase; domain 3 › Topoisomerase, domain 3 0.56 51.0 4.47e-01 100.0% 85.6%
1zc6A02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.55 46.0 3.68e-01 95.9% 55.8%
2h7oA01 1.20.120.1330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Rac1-binding domain, N-terminal GTPase binding subdomain 0.55 44.0 3.70e-01 86.3% 75.6%
1b5lA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.55 48.0 3.85e-01 100.0% 92.8%
4ceiA03 6.10.250.2380 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.54 48.0 4.20e-01 100.0% 90.2%
4hz4A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.53 45.0 3.94e-01 94.5% 90.2%
3eslA01 1.20.58.2070 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.53 37.0 3.69e-01 72.6% 86.7%
4bpxD00 1.20.930.80 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › 0.53 48.0 3.42e-01 100.0% 99.1%
3edvB01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.53 44.0 3.62e-01 93.2% 72.1%
1b48A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.51 43.0 3.80e-01 93.2% 63.3%
1fs0G02 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.51 44.0 4.14e-01 100.0% 80.9%
ECOD (32)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4129856 632.15.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) 0.85 54.0 5.11e-01 100.0% 55.3%
4209005 632.15.1.4 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) › HSP70 0.85 53.0 5.18e-01 100.0% 58.7%
3808173 2484.1.1.1 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HSP70 0.84 53.0 5.31e-01 98.6% 62.7%
4136110 632.7.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › HSP70 0.82 51.0 5.11e-01 97.3% 61.3%
4952624 3843.1.1.29 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › DUF2105 0.76 48.0 4.57e-01 93.2% 55.3%
3974601 601.3.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain 0.73 65.0 5.66e-01 98.6% 89.1%
3715000 632.7.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain 0.71 45.0 4.16e-01 100.0% 49.5%
5016324 601.3.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain 0.68 38.0 3.44e-01 84.9% 42.1%
4044489 632.7.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › HSP70 0.68 46.0 4.39e-01 98.6% 60.0%
4034406 632.15.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) › CompInhib_SCIN 0.68 48.0 4.59e-01 100.0% 63.5%
4934610 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.67 47.0 4.50e-01 100.0% 62.4%
4683346 5041.1.1.1 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › ATP-synt_C 0.67 45.0 4.43e-01 98.6% 64.6%
5003109 1079.1.1.1 ↗ alpha complex topology › Transmembrane reductase CcdA › Transmembrane reductase CcdA › Transmembrane reductase CcdA › DsbD 0.67 60.0 4.23e-01 100.0% 64.0%
4365052 5041.1.1.1 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › ATP-synt_C 0.66 45.0 4.12e-01 98.6% 53.7%
4971634 159.1.1.1 ↗ alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › Hypothetical protein AF_0060 › MazG 0.65 46.0 4.11e-01 98.6% 52.4%
3949790 150.5.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › WXG100 0.65 55.0 4.87e-01 100.0% 66.0%
3471868 6171.1.1.1 ↗ alpha bundles › C-terminal helical domain in Jumonji domain-containing histone demethylases › C-terminal helical domain in Jumonji domain-containing histone demethylases › C-terminal helical domain in Jumonji domain-containing histone demethylases › JHD 0.64 45.0 3.90e-01 95.9% 47.0%
3431415 6155.1.1.6 ↗ alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › DUF2921 0.63 46.0 4.34e-01 75.3% 91.8%
1495253 150.5.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › WXG100 0.62 52.0 4.65e-01 100.0% 66.0%
3962893 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.61 47.0 4.35e-01 98.6% 64.2%
5071125 632.1.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain › Alpha-mann_mid 0.60 40.0 3.58e-01 100.0% 47.6%
4596030 5086.1.1.218 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › MSP1_C 0.60 54.0 4.68e-01 100.0% 78.2%
3975961 5058.1.1.88 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › MS_channel_TM1 0.59 53.0 4.71e-01 100.0% 70.0%
3227678 632.1.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.59 42.0 3.86e-01 97.3% 56.0%
4086054 109.3.1.2 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › Ank,Ank_2 0.59 49.0 3.21e-01 90.4% 26.0%
3222274 198.1.1.3 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_1 0.57 47.0 4.29e-01 90.4% 82.0%
3929572 6155.1.1.2 ↗ alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › PQ-loop 0.57 43.0 4.09e-01 79.5% 100.0%
3491128 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.56 51.0 4.17e-01 100.0% 79.2%
4324180 3755.4.1.0 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.55 49.0 4.45e-01 100.0% 85.0%
3491263 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.54 40.0 3.11e-01 80.8% 66.9%
5054606 7516.1.1.26 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glyco_tranf_2_3 0.52 46.0 2.96e-01 100.0% 82.4%
3677546 109.1.1.6 ↗ alpha superhelices › Repetitive alpha hairpins › Glutathione S-transferase (GST)-C › Glutathione S-transferase (GST)-C › GST_C_2 0.52 43.0 3.54e-01 94.5% 71.4%
D2 medium residues 1-79_158-239
PDB
Domain cluster: rep: Hypothetical_protein_SPPV_50__NP_659626__Sheeppox_virus__10266__D1-82_143-236
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF00752.24 best XPG_N 25.8 1.70e-05 57.8% 90.1%
PF00867.24 XPG_I 31.4 2.80e-07 41.0% 47.7%
D3 medium residues 240-307
PDB
Domain cluster: rep: IMGVR_UViG_3300002053_001336-3300002053-SMTZ23_100214334__D204-271