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ribonucleotide_reductase_subunit_1

Euk-Vir

Leporid_alphaherpesvirus_4

ribonucleotide_reductase_subunit_1__YP_009230170__Leporid_alphaherpesvirus_4__481315

Identity

Accession:
YP_009230170 ↗
Protein ID:
ribonucleotide_reductase_subunit_1
Kingdom:
euk

Quality

87.3 mean pLDDT

3D Structure

Domains

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

D1 high residues 335-348_364-530
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02867.21 best Ribonuc_red_lgC 137.8 6.60e-40 98.9% 33.4%
D2 medium residues 62-200
PDB
Domain cluster: representative
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5cy5B00 1.20.1200.10 Mainly Alpha › Up-down Bundle › Hypothetical Protein Ta1238; Chain: A; › Cobalamin adenosyltransferase-like 0.73 36.0 3.59e-01 77.0% 45.0%
4o6mA02 1.20.120.1760 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CDP-alcohol phosphotransferase transmembrane (TM) domain 0.68 49.0 4.41e-01 74.8% 82.6%
1v9mA01 1.10.132.50 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › ATP synthase (C/AC39) subunit, domain 3 0.60 34.0 3.69e-01 78.4% 64.3%
2mx8A01 1.10.274.70 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Spidroin, N-terminal domain 0.58 34.0 3.73e-01 86.3% 69.9%
1n5uA05 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.56 39.0 4.26e-01 87.8% 88.4%
2radA03 1.20.1440.30 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Biosynthetic Protein domain 0.56 40.0 4.16e-01 89.9% 81.1%
2rgnB01 1.20.900.10 Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain 0.55 38.0 3.32e-01 70.5% 93.1%
3ajmB02 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.54 40.0 4.13e-01 87.1% 80.5%
3vr4B04 1.10.1140.10 Mainly Alpha › Orthogonal Bundle › Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 › Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 0.53 41.0 4.03e-01 81.3% 86.1%
6qumA04 1.10.1140.10 Mainly Alpha › Orthogonal Bundle › Bovine Mitochondrial F1-ATPase, ATP Synthase Beta Chain; Chain D, domain3 › Bovine Mitochondrial F1-atpase; Atp Synthase Beta Chain; Chain D, domain 3 0.53 41.0 4.01e-01 80.6% 85.9%
1nktA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 43.0 3.47e-01 92.1% 88.3%
2nr9A00 1.20.1540.10 Mainly Alpha › Up-down Bundle › Rhomboid-like fold › Rhomboid-like 0.51 40.0 3.65e-01 85.6% 91.7%
2w3cA01 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.50 44.0 3.59e-01 96.4% 52.1%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3365580 601.1.2.3 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › GCIP_C 0.78 58.0 5.30e-01 77.0% 84.8%
3832341 601.1.2.3 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › GCIP_C 0.76 57.0 5.02e-01 77.0% 90.3%
None 0.75 56.0 5.26e-01 77.0% 89.7%
3416038 174.1.1.0 few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.64 38.0 3.97e-01 76.3% 63.1%
5015913 604.5.1.2 alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › PhoU 0.57 46.0 4.10e-01 89.2% 90.0%
3617151 109.4.1.17 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Cullin 0.55 44.0 3.18e-01 84.2% 52.2%
4414070 109.4.1.179 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Nro1 0.54 43.0 3.66e-01 84.2% 82.6%
5027309 160.1.1.4 alpha superhelices › C-terminal domain of alpha and beta subunits of F1 ATP synthase › C-terminal domain of alpha and beta subunits of F1 ATP synthase › C-terminal domain of alpha and beta subunits of F1 ATP synthase › ATP-synt_VA_C 0.53 41.0 4.04e-01 81.3% 86.7%
4066866 109.4.1.179 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Nro1 0.52 42.0 3.12e-01 87.8% 54.8%
D3 medium residues 201-329
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00317.27 best Ribonuc_red_lgN 56.4 3.40e-15 66.7% 94.8%
D4 medium residues 349-363_558-638
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02867.21 best Ribonuc_red_lgC 68.4 7.20e-19 92.7% 15.7%
D5 medium residues 639-716
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02867.21 best Ribonuc_red_lgC 48.8 6.10e-13 100.0% 14.3%
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1r1rA02 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.87 82.0 4.85e-01 100.0% 16.2%
1peqA02 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.84 79.0 4.72e-01 100.0% 19.9%
4rngC00 1.20.1280.290 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.73 61.0 6.06e-01 92.3% 95.2%
2odvA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.68 57.0 5.08e-01 92.3% 92.0%
4x5mA00 1.20.1280.290 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.64 52.0 5.09e-01 92.3% 91.9%
3axjB02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.63 50.0 4.87e-01 85.9% 83.5%
6vydA01 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.62 49.0 3.33e-01 87.2% 24.8%
3dcfA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.61 51.0 4.18e-01 92.3% 73.9%
3vldA01 1.25.10.50 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › 0.60 44.0 3.01e-01 85.9% 20.1%
3nb0B03 6.10.260.10 Special › Helix non-globular › F1FO ATP Synthase › 0.60 38.0 3.70e-01 100.0% 59.5%
2ehgA00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.58 51.0 4.17e-01 98.7% 73.2%
2hyjA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.58 50.0 4.12e-01 97.4% 82.3%
7m7iA02 3.30.70.3290 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 37.0 3.86e-01 80.8% 68.9%
1qv9A02 6.10.140.120 Special › Helix non-globular › Helix Hairpins › 0.58 39.0 3.57e-01 71.8% 52.4%
8cdaC01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.57 45.0 3.94e-01 85.9% 68.4%
4azcA02 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.55 31.0 3.49e-01 70.5% 72.9%
3qbmB00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.53 43.0 3.29e-01 89.7% 45.7%
2fywA01 3.40.1390.30 Alpha Beta › 3-Layer(aba) Sandwich › Udp-n-acetylmuramoylalanyl-d-glutamate--2,6- Diaminopimelate Ligase; Chain: A, domain 1 › NIF3 (NGG1p interacting factor 3)-like 0.53 37.0 3.15e-01 80.8% 43.8%
2hkvA01 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.53 47.0 3.86e-01 100.0% 90.1%
2wssW01 1.10.520.20 Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › N-terminal domain of the delta subunit of the F1F0-ATP synthase 0.52 35.0 3.35e-01 70.5% 97.9%
3t34A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 35.0 2.34e-01 70.5% 40.0%
4h3tA02 1.10.132.100 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › 0.52 45.0 3.77e-01 100.0% 95.0%
2efkA01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.52 46.0 3.21e-01 100.0% 81.3%
2oifB00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.51 40.0 3.36e-01 88.5% 90.1%
ECOD (21)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4822330 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 0.94 90.0 5.35e-01 100.0% 17.2%
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 0.85 80.0 4.68e-01 100.0% 17.1%
3314530 604.3.1.0 alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.69 57.0 5.25e-01 89.7% 81.0%
3968965 604.3.1.0 alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.68 56.0 5.37e-01 91.0% 83.3%
3338608 6155.1.1.2 alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › PQ-loop 0.68 56.0 4.58e-01 92.3% 66.7%
3189488 6155.1.1.0 alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter 0.68 56.0 4.97e-01 89.7% 72.7%
3404235 6155.1.1.1 alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › MtN3_slv 0.66 55.0 4.74e-01 92.3% 66.4%
3723517 6155.1.1.2 alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › PQ-loop 0.65 53.0 5.24e-01 91.0% 94.1%
4887542 604.27.1.0 alpha bundles › Spectrin repeat-like › Triple-helical domain in insecticidal protein Cry1Ac › Triple-helical domain in insecticidal protein Cry1Ac 0.65 53.0 5.49e-01 91.0% 93.2%
5039732 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.64 52.0 4.59e-01 88.5% 92.9%
3246935 5057.1.1.1 alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neur_chan_memb 0.63 52.0 3.95e-01 92.3% 45.3%
3415933 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.62 43.0 3.45e-01 71.8% 55.3%
3730497 6155.1.1.4 alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › MPC 0.60 50.0 4.48e-01 92.3% 69.1%
3361554 604.15.1.0 alpha bundles › Spectrin repeat-like › Efb C-domain-like › Efb C-domain-like 0.59 53.0 4.26e-01 98.7% 72.4%
4994772 5059.1.1.1 alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA 0.57 43.0 3.03e-01 84.6% 88.8%
3702110 593.1.1.0 alpha bundles › GroEL equatorial domain-like › GroEL equatorial domain-like › GroEL equatorial domain-like 0.56 45.0 3.16e-01 87.2% 84.9%
3182290 174.1.1.4 few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › DUF4267 0.54 45.0 3.86e-01 92.3% 69.2%
3389032 5050.1.1.6 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › OATP 0.54 48.0 3.33e-01 100.0% 75.3%
4480231 1002.1.1.1 alpha complex topology › Fluoride ion channel › Fluoride ion channel › Fluoride ion channel › CRCB 0.54 42.0 3.74e-01 84.6% 85.5%
3783902 604.33.1.5 alpha bundles › Spectrin repeat-like › Repulsive guidance molecule (RGM) N-terminal domain › Repulsive guidance molecule (RGM) N-terminal domain › PF29141 0.52 42.0 4.44e-01 93.6% 100.0%
4641463 5050.1.1.54 alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Mntp 0.50 39.0 3.07e-01 88.5% 96.8%
D6 medium residues 723-869
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02867.21 best Ribonuc_red_lgC 103.9 1.20e-29 97.3% 25.4%
CATH (4)
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 70.0 4.41e-01 100.0% 18.0%
5z5cA02 3.40.50.1100 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.62 27.0 3.11e-01 92.5% 52.8%
4f3hA00 3.20.20.450 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › EAL domain 0.57 39.0 3.30e-01 100.0% 42.1%
5xgbA03 3.20.20.450 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › EAL domain 0.54 39.0 3.28e-01 100.0% 44.2%
ECOD (11)
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 0.91 83.0 5.32e-01 100.0% 24.0%
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 83.0 5.33e-01 100.0% 24.4%
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 0.89 70.0 4.54e-01 100.0% 21.9%
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 79.0 5.07e-01 100.0% 23.1%
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 0.87 65.0 4.25e-01 100.0% 21.0%
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 0.84 75.0 4.92e-01 100.0% 25.3%
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 0.83 65.0 4.28e-01 100.0% 23.1%
4165458 3979.1.1.0 a+b four layers › Mre11 nuclease C-terminal domain › Mre11 nuclease C-terminal domain › Mre11 nuclease C-terminal domain 0.73 31.0 4.52e-01 91.2% 89.2%
5040707 2005.1.1.0 a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.63 32.0 3.14e-01 92.5% 42.4%
153585 2002.5.1.1 a/b barrels › TIM beta/alpha-barrel › EAL domain › EAL domain › EAL 0.57 41.0 3.39e-01 100.0% 41.1%
3594565 2007.1.2.0 a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I 0.53 43.0 3.25e-01 87.8% 43.2%