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ribonucleotide_reductase_subunit_1

Euk-Vir

Spheniscid_alphaherpesvirus_1

ribonucleotide_reductase_subunit_1__YP_009342364__Spheniscid_alphaherpesvirus_1__2560777

Identity

Accession:
YP_009342364 ↗
Protein ID:
ribonucleotide_reductase_subunit_1
Kingdom:
euk

Quality

89.3 mean pLDDT

Taxonomy

Heunggongvirae› Peploviricota› Herviviricetes› Herpesvirales› Orthoherpesviridae› Mardivirus› Spheniscid_alphaherpesvirus_1

TaxID: 2560777

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 8-83
PDB
Domain cluster: representative
CATH (45)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2ykgA03 1.20.1320.30 Mainly Alpha › Up-down Bundle › phosphoenolpyruvate carboxylase, domain 3 › 0.71 61.0 5.04e-01 100.0% 53.4%
6hftA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.70 43.0 3.64e-01 75.0% 37.8%
1r2jA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.69 60.0 4.94e-01 100.0% 75.7%
2fu2A00 1.20.1440.50 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Ta0600-like 0.67 57.0 5.71e-01 97.4% 100.0%
4i17A00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.67 48.0 3.42e-01 76.3% 32.6%
4g1tA03 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.65 44.0 3.10e-01 72.4% 21.9%
2xl4A00 1.20.120.1420 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › LntA helical domain 0.63 46.0 3.73e-01 77.6% 57.8%
2wy4A00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.63 48.0 4.04e-01 84.2% 85.6%
2guzA00 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.63 42.0 4.30e-01 94.7% 73.2%
4uurA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.62 47.0 4.07e-01 82.9% 94.4%
1ux8A00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.61 47.0 4.10e-01 82.9% 95.8%
2rgnB01 1.20.900.10 Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain 0.61 51.0 3.91e-01 100.0% 69.6%
2fbnA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.60 42.0 3.44e-01 75.0% 39.2%
1dd5A01 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.60 44.0 3.91e-01 77.6% 84.4%
2gkmA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.59 46.0 3.92e-01 84.2% 83.5%
1tjcA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.59 40.0 3.78e-01 75.0% 55.8%
2hujA00 1.20.120.440 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › YppE-like 0.59 42.0 3.61e-01 76.3% 60.0%
2odmA00 1.10.287.750 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › SO2669-like 0.59 43.0 4.25e-01 77.6% 84.8%
1s0pA01 1.25.40.330 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Adenylate cyclase-associated CAP, N-terminal domain 0.58 51.0 3.98e-01 100.0% 87.7%
1dlwA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.58 46.0 4.05e-01 86.8% 91.4%
4kwaB00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.58 41.0 3.12e-01 75.0% 41.1%
1xdxA01 3.30.1140.40 Alpha Beta › 2-Layer Sandwich › Ribosomal protein S3 C-terminal domain › Tctex-1 0.58 39.0 3.56e-01 78.9% 53.0%
4r8zA00 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.58 43.0 3.14e-01 80.3% 54.6%
4w4kA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.58 34.0 3.31e-01 100.0% 53.7%
3w6zA02 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 39.0 3.40e-01 71.1% 79.3%
7ru9C01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.57 42.0 2.84e-01 85.5% 22.1%
2hfiA00 1.20.120.440 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › YppE-like 0.57 46.0 3.94e-01 89.5% 62.6%
4od4A02 1.20.120.1780 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › UbiA prenyltransferase 0.56 40.0 3.55e-01 77.6% 58.0%
3k8pC01 1.20.58.1440 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.55 42.0 3.82e-01 82.9% 69.5%
2zttA00 6.10.140.720 Special › Helix non-globular › Helix Hairpins › 0.55 40.0 4.14e-01 97.4% 80.8%
3hwrA02 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 0.55 47.0 4.04e-01 100.0% 74.4%
2uyyA02 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 0.55 38.0 3.27e-01 72.4% 78.9%
2ew2A02 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 0.55 47.0 3.98e-01 100.0% 74.6%
2wzkA03 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.54 41.0 3.66e-01 81.6% 61.8%
8bdqA01 1.50.10.100 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › Chondroitin AC/alginate lyase 0.54 40.0 2.56e-01 77.6% 27.2%
3zojA00 1.20.1080.10 Mainly Alpha › Up-down Bundle › Glycerol uptake facilitator protein › Glycerol uptake facilitator protein. 0.54 45.0 3.15e-01 94.7% 47.1%
2gsqA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.53 37.0 3.35e-01 72.4% 86.1%
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 0.53 37.0 3.21e-01 75.0% 72.3%
3lxzB02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.53 39.0 3.21e-01 77.6% 58.0%
4gbjC02 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 0.52 37.0 3.12e-01 75.0% 68.9%
2efjA01 1.10.1200.270 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Methyltransferase, alpha-helical capping domain 0.52 39.0 3.29e-01 80.3% 73.1%
2gf2A02 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 0.51 41.0 3.47e-01 89.5% 70.9%
1h7cA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.51 35.0 3.21e-01 71.1% 91.3%
7e84A03 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.51 38.0 3.39e-01 100.0% 52.0%
1tt5B02 1.10.10.520 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Ubiquitin activating enzymes (Uba3). Chain: B, domain 2 0.51 39.0 3.98e-01 84.2% 88.3%
ECOD (47)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3963355 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.73 39.0 3.98e-01 100.0% 54.7%
3648868 109.4.1.285 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PSMD12-CSN4_N 0.70 45.0 2.94e-01 75.0% 15.4%
3751245 633.23.1.8 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › DUF4534 0.70 62.0 4.98e-01 100.0% 81.3%
3705589 650.1.1.1 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › DnaJ 0.69 45.0 4.09e-01 94.7% 50.0%
3890423 3758.1.1.0 ↗ alpha bundles › Bacterial hemolysins-like › Bacterial hemolysins › Bacterial hemolysins 0.67 59.0 4.06e-01 100.0% 68.0%
3728950 650.1.1.0 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain 0.67 43.0 4.32e-01 94.7% 65.3%
5045414 2006.1.2.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › DHH phosphoesterases › DHH 0.66 45.0 3.36e-01 71.1% 82.6%
4161991 604.12.1.4 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › ATG1-like_MIT1 0.66 48.0 3.76e-01 76.3% 66.5%
4154170 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.66 50.0 4.27e-01 84.2% 68.5%
4039136 604.12.1.4 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › ATG1-like_MIT1 0.65 47.0 3.66e-01 76.3% 76.4%
3579534 192.29.1.144 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › SK_channel 0.65 50.0 3.79e-01 84.2% 68.6%
4376272 601.2.1.4 ↗ alpha bundles › Four-helical up-and-down bundle › Cytochromes › Cytochromes › Cytochrom_C_2 0.65 48.0 3.97e-01 80.3% 66.2%
5066007 2006.1.2.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › DHH phosphoesterases › DHH 0.64 44.0 3.30e-01 72.4% 80.5%
142265 601.4.1.7 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains › LntA_helical 0.63 46.0 3.73e-01 77.6% 57.8%
4646569 4994.1.1.1 ↗ alpha duplicates or obligate multimers › EF2458-like › EF2458-like › EF2458-like › DUF1507 0.63 46.0 4.31e-01 77.6% 74.7%
3317626 109.4.1.285 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PSMD12-CSN4_N 0.62 45.0 3.02e-01 76.3% 21.7%
3867165 3871.1.1.0 ↗ alpha duplicates or obligate multimers › PHIST › PHIST › PHIST 0.62 49.0 4.06e-01 88.2% 63.6%
4277373 4994.1.1.1 ↗ alpha duplicates or obligate multimers › EF2458-like › EF2458-like › EF2458-like › DUF1507 0.61 45.0 4.27e-01 78.9% 76.3%
3515056 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.61 44.0 3.39e-01 76.3% 44.0%
5014330 148.1.3.402 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › Rad50_zn_hook 0.61 40.0 3.44e-01 100.0% 46.4%
3276672 604.3.1.1 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain › BAG 0.61 45.0 3.74e-01 77.6% 63.8%
5081815 1075.5.1.8 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Multidrug and toxic compound extrusion (MATE) transporter › Multidrug and toxic compound extrusion (MATE) transporter › Polysacc_synt_3 0.61 45.0 3.51e-01 81.6% 45.0%
3670571 5058.1.1.0 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.60 46.0 4.07e-01 81.6% 73.6%
3486748 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.60 46.0 4.12e-01 80.3% 82.9%
3619395 621.1.1.2 ↗ alpha bundles › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Interferon-induced guanylate-binding protein 1 (GBP1), C-terminal domain › Smg8_Smg9 0.60 45.0 4.38e-01 78.9% 80.7%
4288099 106.1.1.3 ↗ alpha arrays › Globin-like › Globin-like › Globin-like › Bac_globin 0.60 46.0 3.90e-01 82.9% 86.0%
3473137 604.9.1.2 ↗ alpha bundles › Spectrin repeat-like › Ribosomal protein S20 › Ribosomal protein S20 › Strabismus 0.60 44.0 4.01e-01 77.6% 69.0%
3536798 633.24.1.4 ↗ alpha bundles › Bromodomain-like › RABEX-5 helical domain › RABEX-5 helical domain › RIN1 0.59 47.0 4.30e-01 85.5% 74.0%
3682819 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.59 43.0 2.90e-01 77.6% 56.4%
3773221 109.3.1.163 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › Ank, Ank_2, Ank_4, Ank_5 0.58 41.0 2.75e-01 75.0% 20.3%
56798 150.7.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › PE › PE 0.58 34.0 3.42e-01 100.0% 57.9%
3530124 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.58 44.0 4.35e-01 81.6% 80.0%
5040767 3651.1.1.0 ↗ alpha bundles › Translation initiation factor eIF-2B delta subunit N-terminal helical domain › Translation initiation factor eIF-2B delta subunit N-terminal helical domain › Translation initiation factor eIF-2B delta subunit N-terminal helical domain 0.57 46.0 4.43e-01 85.5% 77.6%
3710128 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.57 45.0 3.04e-01 82.9% 56.0%
4247950 4994.1.1.1 ↗ alpha duplicates or obligate multimers › EF2458-like › EF2458-like › EF2458-like › DUF1507 0.57 42.0 3.91e-01 77.6% 73.7%
1548122 601.43.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › Biofilm formation modulator YmoB › Biofilm formation modulator YmoB › YbaJ 0.57 42.0 3.69e-01 81.6% 61.5%
5048828 2006.1.2.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › DHH phosphoesterases › DHH 0.57 39.0 2.88e-01 76.3% 26.2%
3536764 101.1.11.98 ↗ alpha arrays › HTH › HTH › Ribbon-helix-helix › Pescadillo_N 0.56 43.0 3.96e-01 82.9% 72.0%
5060830 2006.1.2.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › DHH phosphoesterases › DHH 0.56 40.0 3.03e-01 76.3% 35.1%
3865345 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.55 39.0 2.80e-01 77.6% 23.7%
4992953 2006.1.2.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › DHH phosphoesterases › DHH 0.55 47.0 3.49e-01 98.7% 67.1%
3237760 109.24.1.7 ↗ alpha superhelices › Repetitive alpha hairpins › Helical domain in dedicator of cytokinesis protein 9 › Helical domain in dedicator of cytokinesis protein 9 › DHR-2_Lobe_A, PF28208 0.55 45.0 2.53e-01 89.5% 11.1%
3280176 191.1.1.0 ↗ alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain 0.53 38.0 3.27e-01 76.3% 63.1%
4945781 2006.1.2.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › DHH phosphoesterases 0.53 45.0 3.40e-01 100.0% 69.5%
3285767 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.53 41.0 3.67e-01 85.5% 79.8%
4948515 2006.1.2.1 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › DHH phosphoesterases › DHH 0.53 44.0 3.42e-01 98.7% 74.7%
3464184 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.52 36.0 3.30e-01 73.7% 50.9%
D2 medium residues 99-186
PDB
Domain cluster: rep: ribonucleotide_reductase_subunit_1__NP_077434__Cercopithecine_alphaherpesvirus_9__35246__D89-165
D3 medium residues 187-225_453-639_712-729
PDB
Domain cluster: rep: rr1__YP_009552690__Operophtera_brumata_nucleopolyhedrovirus__1046267__D445-618_684-706
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02867.21 best Ribonuc_red_lgC 194.2 5.20e-57 89.3% 34.9%
D4 medium residues 226-340_413-452
PDB
Domain cluster: rep: IMGVR_UViG_3300028089_000252-3300028089-Ga0255299_10029802__D277-388_452-478
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF02867.21 best Ribonuc_red_lgC 77.4 1.30e-21 74.2% 22.1%
PF02867.21 Ribonuc_red_lgC 37.3 1.90e-09 27.1% 7.6%
D5 medium residues 640-711
PDB
Domain cluster: rep: ribonucleotide_reductase_subunit_1__YP_182368__Gallid_alphaherpesvirus_1__10386__D639-699