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ribonucleotide_reductase_large_subunit

Euk-Vir

Esparto_virus

ribonucleotide_reductase_large_subunit__YP_009551741__Esparto_virus__2072209

Identity

Accession:
YP_009551741 ↗
Protein ID:
ribonucleotide_reductase_large_subunit
Kingdom:
euk

Quality

72.9 mean pLDDT

Taxonomy

Naldaviricetes› Lefavirales› Nudiviridae› Alphanudivirus› Esparto_virus

TaxID: 2072209

Cluster

View cluster (25 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 medium residues 20-125
PDB
Domain cluster: rep: RR1__YP_009553087__Drosophila_innubila_nudivirus__2057187__D128-232
D2 medium residues 209-406
PDB
Domain cluster: rep: IMGVR_UViG_3300042092_000730-3300042092-Ga0453238_010587_859_2079__D220-402
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02867.21 best Ribonuc_red_lgC 78.2 7.80e-22 100.0% 35.5%
CATH (53)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2wghA00 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.91 88.0 5.87e-01 100.0% 31.5%
1r1rA02 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.88 85.0 6.06e-01 100.0% 40.8%
1xjkA00 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.84 71.0 4.82e-01 100.0% 27.6%
1peqA02 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.78 59.0 4.27e-01 100.0% 31.6%
6p8vA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.62 36.0 3.51e-01 93.4% 52.1%
2c4kA02 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.61 37.0 4.43e-01 92.9% 87.4%
6ei9A01 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.59 47.0 4.51e-01 99.0% 73.2%
4ja0D02 3.40.50.1970 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.58 34.0 4.14e-01 95.5% 89.1%
7fc0E01 3.20.20.150 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Divalent-metal-dependent TIM barrel enzymes 0.57 45.0 4.09e-01 97.0% 61.8%
1cecA00 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.57 53.0 4.43e-01 100.0% 69.2%
3mbdA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.57 45.0 3.79e-01 97.5% 49.1%
6fnuA00 3.20.20.220 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › 0.57 48.0 4.19e-01 97.0% 60.1%
4o53A00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.56 42.0 3.91e-01 97.5% 60.6%
4o1hA00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.56 31.0 3.94e-01 98.0% 89.9%
3tr2B00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.56 46.0 4.45e-01 100.0% 77.4%
2qs7A00 3.40.1260.10 Alpha Beta › 3-Layer(aba) Sandwich › Hypothetical Protein Ychn; Chain: A, › DsrEFH-like 0.55 36.0 4.25e-01 98.5% 93.5%
4yztA01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.55 51.0 4.33e-01 99.0% 66.6%
2pgeA02 3.20.20.120 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Enolase-like C-terminal domain 0.55 45.0 4.30e-01 100.0% 73.8%
3h4xA00 3.20.20.190 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Phosphatidylinositol (PI) phosphodiesterase 0.55 51.0 4.33e-01 100.0% 83.2%
5jvkA01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.54 50.0 4.26e-01 100.0% 68.8%
4ijrA00 3.20.20.100 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › NADP-dependent oxidoreductase domain 0.54 50.0 4.21e-01 100.0% 86.9%
1fobA00 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.54 50.0 4.18e-01 100.0% 68.6%
4wiwD01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.54 48.0 4.24e-01 98.5% 66.8%
2vx7A00 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.53 49.0 4.01e-01 100.0% 72.5%
7xjrA01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.53 48.0 4.24e-01 100.0% 66.7%
1eucA02 3.40.50.261 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Succinyl-CoA synthetase domains 0.53 41.0 4.45e-01 92.9% 94.1%
1q14A01 3.40.50.1220 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › TPP-binding domain 0.53 38.0 3.94e-01 100.0% 77.4%
3cuxA01 3.20.20.360 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Malate synthase, domain 3 0.53 49.0 3.96e-01 100.0% 70.5%
2nq5A01 3.20.20.210 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › 0.53 49.0 3.90e-01 100.0% 81.1%
5k9xA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.53 46.0 4.23e-01 100.0% 71.3%
2x7vA00 3.20.20.150 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Divalent-metal-dependent TIM barrel enzymes 0.53 48.0 4.26e-01 99.5% 82.9%
3pztB00 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.52 49.0 4.23e-01 100.0% 68.6%
3hpxA01 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.52 48.0 4.18e-01 100.0% 73.8%
4xymC03 3.40.50.261 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Succinyl-CoA synthetase domains 0.52 36.0 3.86e-01 93.9% 81.7%
2pozA02 3.20.20.120 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Enolase-like C-terminal domain 0.52 46.0 4.18e-01 100.0% 72.3%
3iacC01 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.52 45.0 3.61e-01 98.0% 48.8%
3aamA00 3.20.20.150 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Divalent-metal-dependent TIM barrel enzymes 0.52 47.0 4.28e-01 99.5% 82.9%
6h0cA02 3.40.50.360 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Flavodoxin domain 0.52 35.0 3.97e-01 98.5% 90.1%
1lu4A00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.51 27.0 3.19e-01 100.0% 72.4%
1d8wC00 3.20.20.150 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Divalent-metal-dependent TIM barrel enzymes 0.51 48.0 3.75e-01 100.0% 50.4%
2r6hA02 3.40.50.80 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module 0.51 31.0 3.91e-01 99.0% 100.0%
1aogA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.51 29.0 3.64e-01 93.4% 90.9%
1zlpA00 3.20.20.60 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Phosphoenolpyruvate-binding domains 0.51 47.0 4.18e-01 100.0% 70.4%
3dmyA03 3.40.50.261 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Succinyl-CoA synthetase domains 0.51 38.0 4.16e-01 92.9% 92.0%
2fepA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.51 31.0 3.57e-01 95.5% 82.9%
3egcD02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.51 29.0 3.50e-01 95.5% 85.3%
4emyA02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.51 42.0 3.96e-01 97.0% 72.7%
1jeoA00 3.40.50.10490 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glucose-6-phosphate isomerase like protein; domain 1 0.50 34.0 3.58e-01 100.0% 74.6%
5jx5A00 3.20.20.40 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › 1, 4-beta cellobiohydrolase 0.50 46.0 3.93e-01 100.0% 73.3%
2xvlA03 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.50 46.0 3.72e-01 98.0% 65.8%
1brmA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.50 30.0 3.41e-01 97.5% 76.2%
2bb0A02 3.20.20.140 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases 0.50 46.0 4.03e-01 100.0% 75.8%
4f1jA00 3.40.50.410 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › von Willebrand factor, type A domain 0.50 36.0 3.61e-01 98.0% 71.5%
ECOD (46)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3823652 2500.1.1.2 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.91 89.0 6.10e-01 100.0% 35.9%
4015532 2500.1.1.0 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel 0.91 88.0 6.04e-01 100.0% 35.3%
4298539 2500.1.1.2 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.90 87.0 6.11e-01 100.0% 38.5%
996122 2500.1.1.2 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.89 86.0 5.92e-01 100.0% 34.7%
4067125 2500.1.1.2 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.89 86.0 6.13e-01 100.0% 41.2%
4994375 2500.1.1.0 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel 0.89 77.0 5.47e-01 100.0% 35.0%
4993733 2500.1.1.0 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel 0.88 76.0 5.29e-01 100.0% 31.8%
3963206 2500.1.1.2 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.88 85.0 5.97e-01 100.0% 38.4%
4145444 2500.1.1.2 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.88 85.0 6.01e-01 100.0% 39.2%
3942765 2500.1.1.2 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.88 85.0 5.99e-01 100.0% 39.1%
5063882 1074.1.1.6 ↗ alpha arrays › Alpha helical domain of ribonucleotide reductases › Alpha helical domain of ribonucleotide reductases › Alpha helical domain of ribonucleotide reductases › Ribonuc_red_lgC 0.88 74.0 5.88e-01 100.0% 47.9%
4934525 2500.1.1.2 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.88 76.0 5.31e-01 100.0% 32.3%
4985374 2500.1.1.2 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.88 76.0 5.20e-01 100.0% 30.4%
3590466 2500.1.1.2 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.88 84.0 5.89e-01 100.0% 39.8%
3958480 2500.1.1.2 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.87 84.0 6.58e-01 99.5% 58.4%
2504767 2500.1.1.2 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.87 84.0 5.98e-01 100.0% 39.2%
4990406 2500.1.1.2 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.86 83.0 5.70e-01 100.0% 37.1%
5040104 2500.1.1.2 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.86 75.0 5.35e-01 100.0% 34.9%
4564490 2500.1.1.2 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.85 74.0 5.18e-01 100.0% 32.1%
3972491 2500.1.1.2 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.82 79.0 5.47e-01 100.0% 36.7%
4190659 2500.1.1.2 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.82 78.0 5.18e-01 100.0% 29.0%
5058546 2500.1.1.0 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel 0.81 78.0 5.31e-01 100.0% 33.1%
4963031 2500.1.1.2 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.80 77.0 5.24e-01 100.0% 41.3%
4937370 2500.1.1.2 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.79 76.0 5.17e-01 100.0% 38.8%
5030208 2500.1.1.2 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.79 76.0 5.14e-01 100.0% 32.4%
3837967 2004.1.1.138 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DNA_pol3_delta 0.63 36.0 4.06e-01 81.8% 71.3%
3934317 2002.1.1.30 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydro_18 0.58 53.0 4.56e-01 98.0% 67.3%
2833601 2002.1.1.136 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › DUF692 0.57 45.0 4.06e-01 97.0% 60.6%
3170838 2007.1.8.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Uroporphyrinogen III synthase (U3S, HemD) › HEM4 0.56 35.0 4.13e-01 97.5% 91.5%
5071548 2002.1.1.0 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.55 45.0 4.52e-01 91.9% 85.5%
4971215 2002.1.1.120 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.54 50.0 4.05e-01 100.0% 69.0%
5001394 2002.1.1.120 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.54 49.0 4.06e-01 100.0% 56.9%
3943155 2002.1.1.151 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydro_53 0.53 49.0 3.95e-01 100.0% 63.2%
4263032 2006.1.6.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like › VWA 0.53 36.0 3.70e-01 99.0% 71.4%
4933100 2002.1.1.120 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Radical_SAM 0.53 48.0 4.16e-01 98.0% 71.6%
4985931 2002.1.1.70 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glu_synthase 0.52 48.0 3.72e-01 100.0% 53.0%
164356 2002.1.1.174 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › MR_MLE_C 0.52 46.0 4.12e-01 100.0% 69.5%
3389277 2007.1.2.30 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › IR75A_N 0.52 38.0 3.99e-01 97.5% 83.4%
4998574 2002.1.1.99 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › GHL10 0.52 47.0 3.87e-01 98.5% 64.2%
3592644 2002.1.1.0 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.51 47.0 3.92e-01 100.0% 62.3%
4418246 2007.1.3.2 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like › UPF0004 0.51 38.0 4.20e-01 100.0% 96.1%
5037698 2002.1.1.87 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Melibiase 0.51 48.0 4.02e-01 100.0% 80.9%
3470306 2006.1.6.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › vWA-like › VWA 0.51 38.0 3.80e-01 98.0% 75.0%
3278958 7579.1.1.92 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Abhydrolase_1, Abhydrolase_6 0.51 45.0 4.08e-01 98.0% 97.5%
2075143 2002.2.1.1 ↗ a/b barrels › TIM beta/alpha-barrel › Cellulases › Cellulases › Glyco_hydro_6 0.50 46.0 3.93e-01 100.0% 73.3%
4295126 2002.1.1.176 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › PEP_mutase 0.50 47.0 4.08e-01 100.0% 86.6%
D3 medium residues 431-684
PDB
Domain cluster: rep: rr1__YP_009553415__Tomelloso_virus__2053981__D128-178_338-351_396-661_674-684
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02867.21 best Ribonuc_red_lgC 58.5 6.90e-16 77.6% 40.8%