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P3

Euk-Vir

Apium_virus_Y

P3__YP_004123956__Apium_virus_Y__168135

Identity

Accession:
YP_004123956 ↗
Protein ID:
P3
Kingdom:
euk

Quality

79.6 mean pLDDT

Taxonomy

Orthornavirae› Pisuviricota› Stelpaviricetes› Patatavirales› Potyviridae› Potyvirus› Potyvirus_apii

TaxID: 168135

Cluster

View cluster (66 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 1-187
PDB
Domain cluster: rep: P3__YP_009509100__Daphne_virus_Y__282712__D3-191
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF13608.11 best Potyvirid-P3 102.0 5.80e-29 89.8% 33.9%
D2 medium residues 298-352
PDB
Domain cluster: representative
CATH (37)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2eucA00 1.10.8.570 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Hypothetical protein YfmB 0.75 57.0 4.63e-01 85.5% 43.0%
4y66F01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.74 52.0 4.93e-01 87.3% 62.1%
6fhpD00 1.10.390.10 Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 0.72 58.0 5.61e-01 90.9% 95.2%
2oxlA00 1.20.5.5260 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.71 56.0 5.46e-01 90.9% 93.5%
2g9wA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.70 52.0 4.88e-01 83.6% 65.7%
2lh9A00 3.30.420.610 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › LOTUS domain-like 0.69 55.0 4.99e-01 92.7% 64.1%
1ku2A02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.68 55.0 5.47e-01 89.1% 87.7%
4ixjA02 3.30.1690.20 Alpha Beta › 2-Layer Sandwich › TcpA-like pilin › 0.68 58.0 4.27e-01 96.4% 78.2%
2p11A02 1.10.286.50 Mainly Alpha › Orthogonal Bundle › GTP Cyclohydrolase I; Chain A, domain 1 › 0.67 57.0 5.28e-01 100.0% 77.0%
1l0oC00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.67 50.0 5.00e-01 87.3% 78.9%
2vk9A03 1.10.3730.30 Mainly Alpha › Orthogonal Bundle › ProC C-terminal domain-like fold › 0.66 53.0 4.44e-01 90.9% 96.9%
1vtnC00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.65 53.0 4.42e-01 92.7% 52.9%
2qtlA03 3.40.50.80 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module 0.64 44.0 3.21e-01 72.7% 26.5%
4dqlA03 3.40.50.80 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module 0.64 44.0 3.18e-01 72.7% 25.5%
2ma3A00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.64 50.0 4.38e-01 89.1% 59.1%
2ld7B00 1.20.1160.11 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › Paired amphipathic helix 0.64 49.0 4.50e-01 85.5% 80.0%
2mh2A00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.63 51.0 4.89e-01 89.1% 89.1%
4ye6A02 1.10.10.2420 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.62 47.0 4.72e-01 85.5% 89.7%
6muwM00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.62 55.0 3.70e-01 100.0% 66.2%
5xdcB01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.62 54.0 4.32e-01 100.0% 57.7%
2j62A02 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.62 49.0 3.05e-01 89.1% 15.5%
1bqbA02 1.10.390.10 Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › Neutral Protease Domain 2 0.61 50.0 3.78e-01 96.4% 36.1%
2jbrA01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.61 53.0 4.17e-01 100.0% 53.8%
5zorA01 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.61 50.0 4.65e-01 96.4% 72.6%
6muwK00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.61 51.0 3.60e-01 100.0% 49.2%
7tj4A01 1.25.40.1040 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.59 42.0 3.33e-01 76.4% 40.8%
6e5bN00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.58 51.0 3.49e-01 100.0% 50.3%
2hkuB00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.58 46.0 3.32e-01 92.7% 57.3%
2v8pA01 3.30.230.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.58 43.0 3.16e-01 80.0% 85.8%
4fcyA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.58 41.0 3.81e-01 89.1% 56.4%
1uf9A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.57 44.0 3.12e-01 96.4% 25.1%
4z4qA04 1.10.268.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase; domain 3 › Topoisomerase, domain 3 0.57 41.0 3.68e-01 87.3% 50.6%
5xnsC00 1.10.10.580 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Structural maintenance of chromosome 1. Chain E 0.57 50.0 4.58e-01 96.4% 82.9%
7s03A01 1.10.10.1450 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.56 41.0 4.27e-01 89.1% 86.0%
3cueB00 3.30.1380.20 Alpha Beta › 2-Layer Sandwich › Muramoyl-pentapeptide Carboxypeptidase; domain 2 › Trafficking protein particle complex subunit 3 0.54 46.0 3.36e-01 100.0% 82.0%
2qyuA02 1.25.40.300 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Putative secreted effector protein 0.54 44.0 3.08e-01 94.5% 46.7%
1x4qA01 1.20.1390.10 Mainly Alpha › Up-down Bundle › PWI domain › PWI domain 0.54 43.0 4.03e-01 94.5% 77.5%
ECOD (59)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3973557 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.83 68.0 5.35e-01 89.1% 47.3%
2807554 101.1.1.27 ↗ alpha arrays › HTH › HTH › Three-helical HTH › DsrC 0.80 66.0 5.29e-01 89.1% 49.5%
5067843 101.35.1.0 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.79 61.0 6.36e-01 92.7% 92.0%
5063967 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.78 58.0 5.61e-01 87.3% 71.7%
3700443 101.1.1.176 ↗ alpha arrays › HTH › HTH › Three-helical HTH › DEK_C 0.77 55.0 5.25e-01 85.5% 64.6%
4555675 101.1.1.27 ↗ alpha arrays › HTH › HTH › Three-helical HTH › DsrC 0.77 61.0 4.91e-01 89.1% 46.8%
3056106 507.1.1.0 ↗ alpha arrays › DnaB helicase N-terminal domain-related › DnaB helicase N-terminal domain-related › DnaB helicase N-terminal domain-related 0.76 65.0 4.75e-01 96.4% 37.2%
3662896 101.1.1.411 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r2 0.76 55.0 4.14e-01 85.5% 33.6%
3664504 142.1.1.3 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r2 0.75 54.0 3.84e-01 85.5% 26.6%
None — 0.75 54.0 3.87e-01 85.5% 28.0%
3668668 101.1.1.29 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3 0.75 55.0 4.15e-01 87.3% 34.4%
3404553 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.74 53.0 5.03e-01 76.4% 66.2%
4948021 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.73 58.0 5.20e-01 92.7% 61.3%
5046448 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 0.73 57.0 5.57e-01 85.5% 85.0%
3943035 639.2.1.0 ↗ alpha arrays › HHA-like › Regulator of acid resistance influenced by indole (AriR) › Regulator of acid resistance influenced by indole (AriR) 0.72 56.0 5.42e-01 89.1% 87.7%
4452303 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.71 54.0 5.11e-01 87.3% 69.2%
4927329 6049.1.1.0 ↗ alpha bundles › PH0832-like › PH0832-like › PH0832-like 0.71 59.0 5.09e-01 96.4% 66.7%
4952882 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.70 59.0 5.20e-01 94.5% 63.7%
5053497 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.70 56.0 5.52e-01 92.7% 83.3%
3268630 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.70 55.0 4.67e-01 89.1% 53.7%
3579249 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.70 55.0 4.80e-01 87.3% 65.9%
4982795 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.70 54.0 5.21e-01 87.3% 75.4%
4986316 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.69 52.0 4.80e-01 87.3% 61.3%
4059092 101.1.2.27 ↗ alpha arrays › HTH › HTH › winged helix domain › LexA_DNA_bind 0.69 53.0 4.73e-01 87.3% 57.5%
4058877 101.1.2.27 ↗ alpha arrays › HTH › HTH › winged helix domain › LexA_DNA_bind 0.69 53.0 4.97e-01 89.1% 67.1%
3889516 101.1.2.206 ↗ alpha arrays › HTH › HTH › winged helix domain › SAMD1_WH 0.68 53.0 4.36e-01 87.3% 45.7%
4983598 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.68 56.0 5.34e-01 92.7% 78.5%
5014005 614.1.1.0 ↗ alpha duplicates or obligate multimers › L27 domain › L27 domain › L27 domain 0.68 56.0 4.93e-01 90.9% 93.8%
3472278 101.1.2.206 ↗ alpha arrays › HTH › HTH › winged helix domain › SAMD1_WH 0.68 56.0 5.13e-01 94.5% 73.3%
3283630 601.7.1.18 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › HEPN_SAV_6107 0.68 55.0 4.54e-01 96.4% 54.5%
3490008 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.68 56.0 5.36e-01 94.5% 86.2%
3426634 101.1.2.10 ↗ alpha arrays › HTH › HTH › winged helix domain › Linker_histone 0.67 54.0 4.77e-01 92.7% 64.7%
3235055 3065.1.1.2 ↗ alpha bundles › Fatty acid- and retinoid-binding proteins › Fatty acid- and retinoid-binding proteins › Fatty acid- and retinoid-binding proteins › Gp-FAR-1 0.67 56.0 4.17e-01 100.0% 38.1%
3334378 101.35.1.32 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › PF25874 0.66 52.0 5.28e-01 94.5% 90.9%
4665743 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.66 53.0 4.42e-01 94.5% 52.4%
3554511 101.1.2.206 ↗ alpha arrays › HTH › HTH › winged helix domain › SAMD1_WH 0.66 54.0 4.85e-01 94.5% 70.0%
5000777 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.65 55.0 4.65e-01 96.4% 58.5%
None — 0.65 53.0 4.68e-01 94.5% 64.7%
3876302 101.1.2.206 ↗ alpha arrays › HTH › HTH › winged helix domain › SAMD1_WH 0.65 53.0 4.38e-01 94.5% 53.3%
3293154 101.1.2.472 ↗ alpha arrays › HTH › HTH › winged helix domain › A_thal_3526 0.65 52.0 5.08e-01 94.5% 83.3%
3312794 101.1.3.22 ↗ alpha arrays › HTH › HTH › tetra-helical, LuxR-like › A_thal_3526 0.65 52.0 4.74e-01 94.5% 66.7%
3341091 101.35.1.6 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › A_thal_3526 0.64 51.0 4.91e-01 94.5% 76.9%
None — 0.64 52.0 4.70e-01 94.5% 70.0%
4958393 2004.1.1.76 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF87 0.64 51.0 3.22e-01 100.0% 21.8%
3340005 101.1.2.472 ↗ alpha arrays › HTH › HTH › winged helix domain › A_thal_3526 0.63 50.0 4.40e-01 94.5% 56.8%
3404571 101.1.2.206 ↗ alpha arrays › HTH › HTH › winged helix domain › SAMD1_WH 0.63 51.0 4.60e-01 94.5% 68.8%
3334461 101.1.1.270 ↗ alpha arrays › HTH › HTH › Three-helical HTH › A_thal_3526 0.62 50.0 4.61e-01 96.4% 68.0%
3829115 101.1.1.270 ↗ alpha arrays › HTH › HTH › Three-helical HTH › A_thal_3526 0.62 50.0 4.80e-01 96.4% 78.5%
3693234 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.62 52.0 4.77e-01 96.4% 73.3%
4996181 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.62 47.0 4.74e-01 90.9% 89.1%
3504507 610.3.1.3 ↗ alpha arrays › ERP29 C domain-like › GatB/GatE C-terminal domain › GatB/GatE C-terminal domain › tRNA_synt_1c_R1 0.61 47.0 3.35e-01 87.3% 27.6%
3188397 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.61 50.0 4.11e-01 100.0% 96.5%
3400905 210.1.1.1 ↗ a+b four layers › Ntn/PP2C › Ntn › Proteasome subunits › Proteasome 0.60 52.0 3.54e-01 100.0% 46.0%
4322551 604.23.1.0 ↗ alpha bundles › Spectrin repeat-like › Sbi complement-binding domain › Sbi complement-binding domain 0.60 49.0 4.95e-01 92.7% 96.4%
10305 7516.1.1.25 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › TcdA_TcdB 0.59 49.0 2.95e-01 96.4% 86.7%
3201324 210.1.1.1 ↗ a+b four layers › Ntn/PP2C › Ntn › Proteasome subunits › Proteasome 0.59 51.0 3.31e-01 100.0% 39.1%
3715199 2003.1.5.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.57 48.0 2.94e-01 100.0% 17.1%
4975438 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.56 47.0 2.98e-01 98.2% 79.7%
4940618 198.1.1.0 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.53 44.0 3.99e-01 100.0% 83.7%