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HC-Pro_protein

Euk-Vir

Onion_yellow_dwarf_virus

HC-Pro_protein__NP_871739__Onion_yellow_dwarf_virus__43130

Identity

Accession:
NP_871739 ↗
Protein ID:
HC-Pro_protein
Kingdom:
euk

Quality

83.2 mean pLDDT

Taxonomy

Orthornavirae› Pisuviricota› Stelpaviricetes› Patatavirales› Potyviridae› Potyvirus› Onion_yellow_dwarf_virus

TaxID: 43130

Cluster

View cluster (80 members)

3D Structure

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Domains

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

D1 medium residues 30-106
PDB
Domain cluster: rep: HC-Pro__YP_331415__Shallot_yellow_stripe_virus__62059__D30-100
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00851.25 best Peptidase_C6 30.8 2.10e-07 100.0% 15.9%
D2 medium residues 112-181
PDB
Domain cluster: rep: HC-Pro_protein__YP_006405405__Basella_rugose_mosaic_virus__373398__D110-165
CATH (49)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1zoyD00 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.80 56.0 4.95e-01 74.3% 52.0%
2kw6A00 6.10.140.1300 Special › Helix non-globular › Helix Hairpins › 0.77 59.0 6.09e-01 80.0% 95.4%
4nb5B02 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.75 51.0 5.33e-01 71.4% 87.5%
1wp7A00 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.74 50.0 5.25e-01 70.0% 81.2%
4abmD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.74 52.0 5.05e-01 72.9% 76.6%
2y39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.74 50.0 4.30e-01 70.0% 53.6%
6r1nA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.74 52.0 4.53e-01 72.9% 54.4%
3layF00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.73 49.0 4.78e-01 70.0% 71.8%
3t98B00 6.10.140.1350 Special › Helix non-globular › Helix Hairpins › 0.73 52.0 4.90e-01 75.7% 94.2%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.72 49.0 4.91e-01 70.0% 83.1%
3r84A00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.72 50.0 4.82e-01 72.9% 64.2%
7zm7601 1.20.120.1200 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ 0.72 51.0 3.83e-01 74.3% 37.7%
2qe7G01 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.72 50.0 4.43e-01 71.4% 52.6%
1yg2A02 6.10.140.190 Special › Helix non-globular › Helix Hairpins › 0.72 50.0 4.62e-01 72.9% 57.8%
1ku9A02 1.10.287.450 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.72 48.0 5.05e-01 70.0% 78.1%
3lssA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.72 50.0 4.25e-01 72.9% 52.7%
2ic6A00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.71 50.0 4.99e-01 72.9% 74.6%
3f2bA08 1.10.150.870 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.71 51.0 3.96e-01 74.3% 45.3%
8carA01 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.70 52.0 3.27e-01 78.6% 41.0%
3qo8A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.70 49.0 4.25e-01 72.9% 51.9%
2b5uA02 1.10.287.620 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix Hairpins 0.69 48.0 3.67e-01 72.9% 65.2%
1urfA00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.69 48.0 4.65e-01 74.3% 90.1%
2d9dA00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.69 47.0 4.38e-01 71.4% 58.4%
3fd9A03 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.69 46.0 4.60e-01 70.0% 67.1%
2fb5A01 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.68 47.0 4.66e-01 71.4% 75.0%
3ehmA01 1.25.40.390 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.67 51.0 3.24e-01 78.6% 29.4%
3favD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.67 45.0 4.39e-01 70.0% 73.1%
1cxzB00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.66 43.0 4.09e-01 70.0% 54.7%
1qu7A00 1.10.287.950 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Methyl-accepting chemotaxis protein 0.66 45.0 3.18e-01 71.4% 35.2%
1u7lA02 1.20.1460.10 Mainly Alpha › Up-down Bundle › subunit c (vma5p) of the yeast v-atpase, domain 2 › subunit c (vma5p) of the yeast v-atpase, domain 2 0.65 45.0 3.23e-01 71.4% 63.9%
4kx7A04 1.25.50.20 Mainly Alpha › Alpha Horseshoe › Zincin-like fold › 0.64 47.0 3.04e-01 78.6% 27.6%
3tulB00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.63 43.0 3.55e-01 71.4% 39.1%
6vq6G02 1.20.1460.10 Mainly Alpha › Up-down Bundle › subunit c (vma5p) of the yeast v-atpase, domain 2 › subunit c (vma5p) of the yeast v-atpase, domain 2 0.63 44.0 3.21e-01 72.9% 63.6%
1qsdA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 44.0 3.90e-01 72.9% 70.6%
6dcjA02 1.25.40.650 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.62 45.0 3.95e-01 77.1% 54.8%
1kxpD02 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.61 50.0 4.76e-01 95.7% 94.3%
1vt0k00 1.10.3230.20 Mainly Alpha › Orthogonal Bundle › Hypothetical protein yqbg › P22 tail accessory factor (Gp4) 0.60 49.0 4.02e-01 95.7% 64.8%
2yevA02 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.59 40.0 4.01e-01 70.0% 66.2%
6n2nA01 3.40.920.10 Alpha Beta › 3-Layer(aba) Sandwich › Pyruvate-ferredoxin Oxidoreductase; domain 3 › Pyruvate-ferredoxin oxidoreductase, PFOR, domain III 0.59 43.0 3.25e-01 78.6% 92.7%
6xj1A01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.58 47.0 3.28e-01 91.4% 84.9%
7c1iA01 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.57 45.0 4.05e-01 91.4% 60.0%
2pbiA02 1.10.1240.60 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › 0.57 41.0 3.66e-01 75.7% 88.1%
1gcvB00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.57 46.0 3.73e-01 90.0% 84.6%
1c9bA01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.56 42.0 3.85e-01 81.4% 71.1%
6humG01 1.20.120.1200 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ 0.55 45.0 3.52e-01 92.9% 45.6%
2j4bB00 1.25.40.500 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › TFIID subunit TAF5, NTD2 domain 0.55 48.0 3.91e-01 100.0% 100.0%
1sqgA01 1.10.940.10 Mainly Alpha › Orthogonal Bundle › N-utilizing Substance Protein B Homolog; Chain A › NusB-like 0.54 41.0 3.28e-01 80.0% 62.4%
6fakA02 1.10.246.10 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.54 43.0 4.16e-01 88.6% 97.5%
8befJ01 1.20.120.1200 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ 0.52 45.0 3.47e-01 100.0% 100.0%
ECOD (35)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4106620 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 0.79 54.0 5.26e-01 70.0% 74.7%
3482539 192.8.1.288 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › Ada3 0.79 53.0 4.68e-01 70.0% 53.0%
4961961 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 0.77 52.0 5.11e-01 70.0% 69.3%
3477418 4992.1.1.12 ↗ extended segments › RelB-like › RelB-like › RelB-like › LIN9_C 0.76 54.0 4.83e-01 74.3% 91.6%
4937604 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.75 52.0 4.40e-01 72.9% 45.2%
4493879 4992.1.1.23 ↗ extended segments › RelB-like › RelB-like › RelB-like › Seryl_tRNA_N 0.74 50.0 4.30e-01 70.0% 50.9%
3780286 244.1.1.6 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C › Amino_oxidase 0.74 51.0 3.01e-01 72.9% 9.2%
4595410 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.74 50.0 5.18e-01 72.9% 75.4%
4038138 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.74 51.0 4.16e-01 72.9% 61.5%
3184698 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.73 49.0 4.56e-01 70.0% 70.0%
3933048 4992.1.1.12 ↗ extended segments › RelB-like › RelB-like › RelB-like › LIN9_C 0.73 49.0 4.40e-01 70.0% 70.0%
3326073 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.73 51.0 4.37e-01 72.9% 47.3%
1879027 244.1.1.6 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C › Amino_oxidase 0.73 51.0 3.16e-01 72.9% 13.6%
3942242 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.73 50.0 4.02e-01 72.9% 52.1%
3788311 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.72 50.0 4.26e-01 72.9% 45.2%
4500653 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.72 50.0 3.92e-01 72.9% 34.7%
4013459 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.72 51.0 3.12e-01 74.3% 12.7%
4819006 2004.1.1.5 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.71 48.0 3.21e-01 70.0% 17.9%
3906191 4323.1.1.1 ↗ alpha bundles › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C › helical bundle domain in vacuolar ATP synthase subunit C › V_ATPase_I 0.70 49.0 3.79e-01 72.9% 33.5%
4315986 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.70 48.0 4.40e-01 70.0% 54.4%
3840952 601.19.1.39 ↗ alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein › LIN9_C 0.70 49.0 4.81e-01 72.9% 78.7%
3693258 604.7.1.1 ↗ alpha bundles › Spectrin repeat-like › Tubulin chaperone cofactor A › Tubulin chaperone cofactor A › TBCA 0.70 49.0 4.20e-01 72.9% 47.3%
3754639 150.5.1.106 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › LIN9_C 0.70 48.0 4.56e-01 72.9% 65.9%
149872 3291.1.1.1 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Snf7 0.68 46.0 4.43e-01 70.0% 62.0%
3204414 1.1.17.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 0.68 46.0 2.93e-01 71.4% 14.5%
5038395 601.4.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.67 56.0 4.43e-01 95.7% 60.0%
3741609 109.58.1.1 ↗ alpha superhelices › Repetitive alpha hairpins › DNA repair protein Rev1 C-terminal domain › DNA repair protein Rev1 C-terminal domain › REV1_C 0.67 47.0 4.25e-01 74.3% 88.4%
4619538 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.65 43.0 3.70e-01 70.0% 41.7%
5048365 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.61 47.0 3.25e-01 82.9% 42.5%
3470680 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.60 52.0 3.21e-01 95.7% 49.4%
3929573 192.8.1.395 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › CHDCT2 0.60 49.0 4.62e-01 90.0% 98.8%
3685114 605.4.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › ROP protein › ROP protein 0.59 45.0 3.73e-01 80.0% 80.0%
5002258 109.7.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Cytochrome c oxidase subunit E › Cytochrome c oxidase subunit E 0.56 40.0 3.88e-01 77.1% 76.2%
3923696 198.1.1.0 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.55 38.0 3.55e-01 72.9% 95.6%
3494968 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.55 44.0 4.31e-01 94.3% 88.7%
D3 medium residues 203-269
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00851.25 best Peptidase_C6 43.8 2.60e-11 100.0% 15.7%
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3qitB00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.55 39.0 2.62e-01 76.1% 82.0%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3289185 247.1.1.33 ↗ a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Lactamase_B, Lactamase_B_2, Anti-Pycsar_Apyc1 0.52 37.0 2.48e-01 77.6% 68.5%
D4 medium residues 270-460
PDB
Domain cluster: rep: HC-Pro_protein__YP_006590094__Chinese_yam_necrotic_mosaic_virus__128818__D95-261
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00851.25 best Peptidase_C6 233.7 6.00e-69 97.4% 41.1%