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ribonucleoside-diphosphate_reductase_large_chain

Euk-Vir

Lausannevirus

ribonucleoside-diphosphate_reductase_large_chain__YP_004347174__Lausannevirus__999883

Identity

Accession:
YP_004347174 ↗
Protein ID:
ribonucleoside-diphosphate_reductase_large_chain
Kingdom:
euk

Quality

81.3 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Megaviricetes› Pimascovirales› Marseilleviridae› Losannavirus› Lausannevirus

TaxID: 999883

Cluster

View cluster (122 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 235-248_266-396
PDB
Domain cluster: rep: ribonucleotide-diphosphate_reductase_large_chain__YP_009119180__Pandoravirus_inopinatum__1605721__D783-936
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02867.21 best Ribonuc_red_lgC 141.4 5.20e-41 93.8% 24.4%
D2 medium residues 6-71
PDB
Domain cluster: rep: hypothetical_protein_GMAR_ORF126__YP_009310243__Golden_Marseillevirus__1720526__D16-69
D3 medium residues 187-234_249-265
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02867.21 best Ribonuc_red_lgC 26.9 2.70e-06 90.8% 8.0%
CATH (46)
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 85.0 4.77e-01 100.0% 13.0%
1xjkA00 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.89 81.0 4.54e-01 96.9% 17.3%
6jtdA01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.77 57.0 3.70e-01 78.5% 21.8%
2qs7A00 3.40.1260.10 Alpha Beta › 3-Layer(aba) Sandwich › Hypothetical Protein Ychn; Chain: A, › DsrEFH-like 0.76 59.0 4.57e-01 83.1% 66.7%
3aptA00 3.20.20.220 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › 0.75 59.0 3.79e-01 84.6% 22.3%
4rheC00 3.40.50.1950 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Flavin prenyltransferase-like 0.71 54.0 3.76e-01 81.5% 34.3%
4g2tA01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.68 49.0 3.49e-01 78.5% 24.4%
6rqaA02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.68 51.0 3.80e-01 87.7% 31.2%
1ceqA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.68 54.0 4.20e-01 92.3% 40.9%
3tnjA01 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.68 50.0 4.18e-01 81.5% 53.7%
2p6pB01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.67 47.0 3.35e-01 76.9% 23.3%
1reqB02 3.40.50.280 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Cobalamin-binding domain 0.67 51.0 3.97e-01 81.5% 40.3%
3topA03 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.66 49.0 3.09e-01 81.5% 17.7%
2ihuA01 3.40.50.970 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains 0.66 55.0 3.99e-01 93.8% 49.7%
4c6sA00 3.40.50.10140 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Toll/interleukin-1 receptor homology (TIR) domain 0.65 48.0 3.79e-01 80.0% 45.8%
6a6eA02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.65 49.0 3.27e-01 83.1% 20.3%
3gdwB00 3.40.50.510 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphotransferase system, mannose-type IIA component 0.65 48.0 3.85e-01 81.5% 63.0%
6se1A01 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.65 49.0 3.38e-01 84.6% 40.8%
4uulA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.64 54.0 4.09e-01 92.3% 41.4%
4bguA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.64 49.0 3.90e-01 86.2% 49.3%
6k34A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.64 49.0 3.19e-01 84.6% 33.9%
4ry9A01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.63 48.0 3.80e-01 83.1% 60.0%
4ywhA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.62 48.0 3.73e-01 83.1% 55.9%
3hebA00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.62 51.0 4.00e-01 92.3% 64.8%
6ryzC01 3.40.50.10790 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › S-adenosyl-l-methionine hydroxide adenosyltransferase, N-terminal 0.62 46.0 3.50e-01 81.5% 63.2%
3ksmA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.62 46.0 3.76e-01 81.5% 65.9%
4ry8A01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.61 46.0 3.60e-01 83.1% 56.1%
2h3hA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.61 51.0 3.90e-01 92.3% 55.4%
3fniA00 3.40.50.360 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Flavodoxin domain 0.61 47.0 3.69e-01 87.7% 39.6%
1fvpA00 3.20.20.30 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Luciferase-like domain 0.60 49.0 3.40e-01 92.3% 46.8%
4rsmD01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.59 47.0 3.63e-01 92.3% 74.2%
1t9hA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.59 46.0 3.67e-01 90.8% 52.1%
4zqbB01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.59 40.0 3.24e-01 84.6% 35.3%
1dbqA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.58 47.0 3.77e-01 92.3% 90.3%
2i0fA00 3.40.50.960 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Lumazine/riboflavin synthase 0.57 47.0 3.67e-01 92.3% 67.3%
2hqbA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.57 46.0 3.73e-01 90.8% 59.5%
3dl2A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.57 47.0 3.76e-01 95.4% 50.4%
6h0cA02 3.40.50.360 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Flavodoxin domain 0.56 45.0 3.54e-01 92.3% 56.6%
3om0A02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.56 43.0 3.28e-01 84.6% 35.0%
3iibA01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.56 37.0 2.53e-01 70.8% 52.7%
1k68A00 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.55 45.0 3.56e-01 92.3% 61.4%
1tjyA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.54 45.0 3.51e-01 100.0% 74.8%
1twyA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.51 35.0 3.01e-01 73.8% 99.1%
2b3fA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.51 40.0 2.91e-01 87.7% 67.0%
4x9tA01 3.40.190.150 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Bordetella uptake gene, domain 1 0.50 40.0 3.01e-01 89.2% 70.7%
5swvC02 3.40.50.10860 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Leucine Dehydrogenase, chain A, domain 1 0.50 39.0 3.25e-01 92.3% 70.6%
ECOD (21)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
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 0.89 83.0 4.68e-01 98.5% 14.3%
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 0.88 81.0 4.62e-01 98.5% 14.6%
5000617 2006.1.2.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › DHH phosphoesterases › DHH 0.73 54.0 3.56e-01 78.5% 86.9%
4951055 2006.1.2.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › DHH phosphoesterases › DHH 0.71 54.0 3.64e-01 81.5% 87.1%
4474169 7512.1.1.12 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glyco_tran_28_C 0.68 49.0 3.55e-01 78.5% 30.3%
4947642 2007.1.9.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) 0.64 47.0 3.75e-01 80.0% 56.4%
5077967 2004.1.1.120 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ResIII 0.62 47.0 3.61e-01 83.1% 47.7%
3736347 2007.1.3.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like 0.62 48.0 3.71e-01 87.7% 36.9%
4634797 7512.1.1.12 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glyco_tran_28_C 0.61 48.0 3.39e-01 86.2% 27.3%
4663229 7523.1.1.15 ↗ a/b three-layered sandwiches › Periplasmic binding protein-like II › Periplasmic binding protein-like II › Periplasmic binding protein-like II › LysR_substrate 0.59 40.0 2.83e-01 70.8% 65.9%
4075277 7512.1.1.12 ↗ a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glyco_tran_28_C 0.59 48.0 3.43e-01 92.3% 95.6%
3791095 2007.2.1.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › Flavoproteins › Flavodoxin_1 0.58 46.0 3.30e-01 84.6% 94.3%
3411651 7510.1.1.0 ↗ a/b three-layered sandwiches › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like 0.57 47.0 3.54e-01 96.9% 54.4%
4947286 7502.1.1.0 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS 0.56 44.0 3.57e-01 83.1% 68.7%
5059333 2488.1.1.1 ↗ a/b three-layered sandwiches › alpha/beta knot › alpha/beta knot › alpha/beta knot › SpoU_methylase 0.56 44.0 3.14e-01 90.8% 41.8%
4939789 2007.13.1.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Rossmann-like domains in magnesium chelatase catalytic subunit › Rossmann-like domains in magnesium chelatase catalytic subunit 0.55 40.0 3.16e-01 78.5% 67.1%
4014612 2007.1.3.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like 0.54 40.0 3.21e-01 83.1% 44.0%
4110542 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.54 45.0 3.73e-01 90.8% 91.8%
4375036 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.53 43.0 3.70e-01 87.7% 80.0%
4600916 2007.1.6.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Aminoacid dehydrogenase-like, N-terminal domain 0.53 42.0 3.73e-01 92.3% 93.0%
4138280 2007.1.6.4 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Aminoacid dehydrogenase-like, N-terminal domain › Shikimate_dh_N 0.52 41.0 3.68e-01 92.3% 94.0%
D4 medium residues 402-534_604-663
PDB
D5 medium residues 535-603
PDB
Domain cluster: rep: IMGVR_UViG_3300045988_178991-3300045988-Ga0495776_136811_42162_44546__D269-361
D6 medium residues 664-745
PDB
Domain cluster: rep: ribonucleotide_reductase_large_subunit__YP_009220529__White_spot_syndrome_virus__342409__D469-546
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02867.21 best Ribonuc_red_lgC 63.2 2.70e-17 100.0% 14.9%
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4j0eA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.56 47.0 3.51e-01 91.5% 54.0%
1dd5A01 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.55 49.0 4.47e-01 98.8% 87.2%
2vf1A04 1.20.140.120 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › 0.53 39.0 3.21e-01 79.3% 84.7%
1lu4A00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.52 31.0 2.71e-01 100.0% 34.3%
2oayA01 3.30.497.10 Alpha Beta › 2-Layer Sandwich › Antithrombin; Chain I, domain 2 › Antithrombin, subunit I, domain 2 0.50 39.0 3.04e-01 84.1% 61.2%
ECOD (13)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4015532 2500.1.1.0 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel 0.98 92.0 5.31e-01 100.0% 13.9%
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 0.97 85.0 5.31e-01 95.1% 20.8%
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 0.93 87.0 4.94e-01 100.0% 11.8%
5058546 2500.1.1.0 ↗ a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel 0.92 85.0 4.91e-01 100.0% 13.0%
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 0.92 87.0 5.12e-01 100.0% 15.0%
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 0.89 84.0 4.90e-01 100.0% 14.9%
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 74.0 4.67e-01 100.0% 20.0%
2472944 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 77.0 4.67e-01 100.0% 17.6%
4055499 3563.1.1.1 ↗ alpha bundles › Twin arginine protein translocation system component TatC › Twin arginine protein translocation system component TatC › Twin arginine protein translocation system component TatC › TatC 0.60 44.0 3.21e-01 79.3% 70.0%
4028492 2006.1.4.25 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › XPG_I 0.55 46.0 3.36e-01 92.7% 63.0%
4442629 3563.1.1.1 ↗ alpha bundles › Twin arginine protein translocation system component TatC › Twin arginine protein translocation system component TatC › Twin arginine protein translocation system component TatC › TatC 0.53 43.0 3.10e-01 90.2% 29.1%
1396775 4984.1.1.2 ↗ alpha bundles › Duffy-binding-like domain, C-terminal subdomain › Duffy-binding-like domain, C-terminal subdomain › Duffy-binding-like domain, C-terminal subdomain › DBL_C 0.53 46.0 3.59e-01 98.8% 76.5%
4537298 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.51 29.0 2.63e-01 74.4% 39.1%
D7 medium residues 746-855
PDB
Domain cluster: rep: ribonucleoside-diphosphate_reductase_large_chain__YP_009506879__Tunisvirus_fontaine2__1421067__D736-828
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02867.21 best Ribonuc_red_lgC 33.8 2.10e-08 100.0% 13.9%
D8 medium residues 860-1004
PDB
Domain cluster: rep: ribonucleotide_reductase_subunit_1__YP_009230170__Leporid_alphaherpesvirus_4__481315__D723-869
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02867.21 best Ribonuc_red_lgC 100.0 1.90e-28 97.9% 25.8%