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ribonucleoside_diphosphate_reductase

Euk-Vir

Micromonas_pusilla_virus_12T

ribonucleoside_diphosphate_reductase__YP_007676167__Micromonas_pusilla_virus_12T__755272

Identity

Accession:
YP_007676167 ↗
Protein ID:
ribonucleoside_diphosphate_reductase
Kingdom:
euk

Quality

91.9 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Megaviricetes› Algavirales› Phycodnaviridae› Prasinovirus› Micromonas_pusilla_virus_12T

TaxID: 755272

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 2-88
PDB
Domain cluster: rep: KY549443.1__APZ82050.1__EFP01_123__00123__D15-106
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03477.22 best ATP-cone 39.2 1.20e-09 100.0% 96.6%
CATH (27)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1px5A02 1.10.1410.20 Mainly Alpha › Orthogonal Bundle › Poly(a)-polymerase, middle domain › 2'-5'-oligoadenylate synthetase 1, domain 2 0.75 62.0 4.81e-01 89.7% 71.0%
4uurA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.73 49.0 4.38e-01 70.1% 96.8%
3deeA01 1.10.150.690 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › DUF2063 0.69 56.0 5.66e-01 89.7% 96.5%
4k90A02 1.10.390.10 Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 0.69 61.0 4.78e-01 100.0% 94.7%
2nn4A00 1.10.287.760 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YqgQ-like 0.66 44.0 5.08e-01 79.3% 96.8%
3nqxA02 1.10.390.10 Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 0.66 60.0 5.04e-01 100.0% 97.9%
1wpaA01 6.10.140.340 Special › Helix non-globular › Helix Hairpins › 0.66 36.0 3.44e-01 94.3% 44.4%
1rp3A01 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.66 48.0 4.87e-01 75.9% 83.5%
2nrlA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.66 45.0 3.88e-01 72.4% 93.1%
2ffjA01 1.10.8.380 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Uncharacterised protein PF01937, DUF89, domain 1 0.63 40.0 4.60e-01 75.9% 100.0%
3bt5A00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.62 49.0 4.12e-01 86.2% 84.1%
3qa8A04 1.20.1270.250 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.61 35.0 2.55e-01 96.6% 20.2%
4rflA02 1.20.1090.10 Mainly Alpha › Up-down Bundle › Dehydroquinate synthase-like, alpha domain › Dehydroquinate synthase-like - alpha domain 0.60 53.0 4.00e-01 96.6% 73.4%
2gfhA02 1.20.120.710 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Haloacid dehalogenase hydrolase-like domain 0.59 46.0 4.69e-01 86.2% 88.4%
3tu3B03 1.20.1050.100 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.55 44.0 3.58e-01 87.4% 52.9%
1sqgA01 1.10.940.10 Mainly Alpha › Orthogonal Bundle › N-utilizing Substance Protein B Homolog; Chain A › NusB-like 0.55 44.0 3.84e-01 89.7% 65.2%
2fu2A00 1.20.1440.50 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Ta0600-like 0.54 39.0 4.14e-01 77.0% 97.4%
4ls9B01 3.90.1640.10 Alpha Beta › Alpha-Beta Complex › inorganic pyrophosphatase (n-terminal core) › inorganic pyrophosphatase (n-terminal core) 0.54 41.0 3.26e-01 85.1% 75.0%
4jgwA01 1.20.870.10 Mainly Alpha › Up-down Bundle › Son of sevenless (SoS) protein; Chain S, domain 1 › Son of sevenless (SoS) protein Chain: S domain 1 0.53 41.0 3.38e-01 85.1% 46.8%
2kjgA00 1.20.120.970 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.52 37.0 3.63e-01 75.9% 67.7%
1khyD00 1.10.1780.10 Mainly Alpha › Orthogonal Bundle › Double Clp-N motif › Clp, N-terminal domain 0.52 41.0 3.54e-01 85.1% 89.2%
2yjkC00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.52 46.0 3.86e-01 100.0% 74.5%
5af7B03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.51 43.0 3.72e-01 95.4% 86.5%
3jsbA01 1.20.1440.300 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › RNA-directed RNA polymerase L, helical domain 0.51 41.0 4.23e-01 95.4% 95.1%
1agyA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.51 39.0 3.13e-01 87.4% 70.6%
6w6jD01 1.10.1780.10 Mainly Alpha › Orthogonal Bundle › Double Clp-N motif › Clp, N-terminal domain 0.50 39.0 3.46e-01 86.2% 90.8%
1q8cA00 1.10.940.10 Mainly Alpha › Orthogonal Bundle › N-utilizing Substance Protein B Homolog; Chain A › NusB-like 0.50 40.0 3.55e-01 89.7% 75.8%
ECOD (49)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3394718 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 1.00 69.0 8.25e-01 71.3% 100.0%
3486229 103.2.1.0 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone 0.99 96.0 9.53e-01 100.0% 97.8%
3519243 1074.1.1.0 ↗ alpha arrays › Alpha helical domain of ribonucleotide reductases › Alpha helical domain of ribonucleotide reductases › Alpha helical domain of ribonucleotide reductases 0.98 80.0 5.83e-01 83.9% 38.0%
3607359 103.2.1.1 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › Ribonuc_red_lgN 0.98 80.0 5.75e-01 83.9% 36.1%
2320584 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.97 94.0 8.95e-01 100.0% 90.7%
3784313 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.96 90.0 8.95e-01 100.0% 95.6%
3594048 103.2.1.0 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone 0.94 90.0 8.91e-01 100.0% 97.8%
4257906 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.93 89.0 8.78e-01 100.0% 96.7%
4312875 103.2.1.0 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone 0.93 88.0 8.55e-01 100.0% 91.6%
4990404 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.92 83.0 7.83e-01 100.0% 82.0%
2791177 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.91 85.0 7.83e-01 100.0% 81.1%
4994194 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.89 72.0 7.75e-01 94.3% 97.3%
1853272 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.89 83.0 7.92e-01 100.0% 87.9%
4961006 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.89 72.0 7.72e-01 95.4% 98.7%
5043182 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.88 82.0 7.78e-01 98.9% 97.0%
4942297 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.88 67.0 7.38e-01 89.7% 98.6%
1878968 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.87 81.0 7.69e-01 100.0% 86.0%
4987113 103.2.1.0 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone 0.87 71.0 7.63e-01 96.6% 100.0%
4980139 103.2.1.0 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone 0.86 80.0 7.59e-01 97.7% 95.0%
4987957 103.2.1.0 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone 0.86 71.0 7.63e-01 95.4% 100.0%
4485359 103.2.1.0 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone 0.86 76.0 7.40e-01 95.4% 86.3%
5057092 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.86 65.0 7.21e-01 89.7% 98.6%
4954173 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.85 69.0 7.33e-01 95.4% 98.7%
4952141 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.84 69.0 7.15e-01 98.9% 95.0%
4143596 103.2.1.0 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone 0.83 67.0 6.65e-01 85.1% 94.4%
4952067 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.83 58.0 6.64e-01 82.8% 96.9%
4948420 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.83 70.0 7.29e-01 98.9% 97.5%
5017312 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.83 69.0 7.18e-01 100.0% 97.5%
4238441 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.82 71.0 7.42e-01 93.1% 100.0%
4160317 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.82 75.0 6.79e-01 100.0% 74.8%
4056578 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.81 74.0 6.79e-01 97.7% 77.3%
4997983 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.78 63.0 6.78e-01 96.6% 100.0%
4945368 181.1.1.0 ↗ alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins 0.77 65.0 6.79e-01 98.9% 100.0%
5010578 103.2.1.2 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone › ATP-cone 0.76 66.0 6.60e-01 100.0% 92.2%
3610347 103.2.1.0 ↗ alpha arrays › RuvA-C › ATP cone › ATP cone 0.72 58.0 5.94e-01 87.4% 94.1%
3305472 148.1.3.19 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_lid_3 0.63 43.0 4.21e-01 81.6% 64.2%
4520559 592.2.1.1 ↗ alpha arrays › PWI domain-like › YugE-like › YugE-like › DUF1871 0.63 47.0 4.79e-01 87.4% 82.4%
5078022 592.2.1.0 ↗ alpha arrays › PWI domain-like › YugE-like › YugE-like 0.60 47.0 4.85e-01 98.9% 95.0%
3190074 109.4.1.929 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HEAT_ECM29 0.59 49.0 3.37e-01 89.7% 27.0%
4977814 2006.1.4.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.59 47.0 3.85e-01 86.2% 95.2%
143247 592.2.1.1 ↗ alpha arrays › PWI domain-like › YugE-like › YugE-like › DUF1871 0.59 45.0 4.66e-01 88.5% 89.0%
5001078 633.2.1.0 ↗ alpha bundles › Bromodomain-like › Carnobacteriocin B2 immunity protein › Carnobacteriocin B2 immunity protein 0.58 42.0 4.12e-01 77.0% 87.4%
3456399 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.57 44.0 3.72e-01 82.8% 61.3%
3936950 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.57 49.0 4.71e-01 100.0% 82.0%
3179442 109.4.1.356 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Fungal_trans 0.54 47.0 2.99e-01 92.0% 24.7%
4956162 4995.1.1.0 ↗ alpha arrays › Methionine synthase domain-like › Methionine synthase domain-like › Methionine synthase domain-like 0.54 43.0 4.56e-01 87.4% 100.0%
4267135 633.2.1.0 ↗ alpha bundles › Bromodomain-like › Carnobacteriocin B2 immunity protein › Carnobacteriocin B2 immunity protein 0.54 42.0 4.31e-01 87.4% 92.9%
3416922 109.4.1.1199 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_Nup160_C 0.52 44.0 3.14e-01 89.7% 37.1%
3589212 633.2.1.1 ↗ alpha bundles › Bromodomain-like › Carnobacteriocin B2 immunity protein › Carnobacteriocin B2 immunity protein › EntA_Immun 0.51 38.0 4.07e-01 92.0% 96.0%
D2 medium residues 104-198_432-459
PDB
Domain cluster: rep: NC_007021.1__YP_238596.1__TwortORF045__00062__D44-158
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00317.27 best Ribonuc_red_lgN 82.6 2.40e-23 59.4% 98.7%
D3 medium residues 199-318_389-431
PDB
Domain cluster: rep: ribonucleotide_reductase_large_subunit__YP_009702292__African_swine_fever_virus__10497__D187-309_381-436_716-757
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF02867.21 best Ribonuc_red_lgC 156.2 1.70e-45 72.4% 22.1%
PF02867.21 Ribonuc_red_lgC 55.1 7.90e-15 28.8% 9.2%
D4 medium residues 319-388
PDB
Domain cluster: rep: IMGVR_UViG_3300007266_000133-3300007266-Ga0101450_1063125__D8-101
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02867.21 best Ribonuc_red_lgC 78.9 4.50e-22 100.0% 13.4%
D5 medium residues 460-612_674-732
PDB
Domain cluster: rep: rr1__YP_009552690__Operophtera_brumata_nucleopolyhedrovirus__1046267__D445-618_684-706
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF02867.21 best Ribonuc_red_lgC 181.6 3.40e-53 74.1% 29.6%
PF02867.21 Ribonuc_red_lgC 64.6 1.00e-17 26.9% 10.7%
D6 medium residues 613-673
PDB
Domain cluster: rep: IMGVR_UViG_3300006567_000026-3300006567-Ga0099958_11086953__D213-268
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02867.21 best Ribonuc_red_lgC 45.5 6.10e-12 100.0% 11.5%