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P3

Euk-Vir

Narcissus_late_season_yellows_virus

P3__YP_009010961__Narcissus_late_season_yellows_virus__160842

Identity

Accession:
YP_009010961 ↗
Protein ID:
P3
Kingdom:
euk

Quality

79.5 mean pLDDT

Taxonomy

Orthornavirae› Pisuviricota› Stelpaviricetes› Patatavirales› Potyviridae› Potyvirus› Narcissus_late_season_yellows_virus

TaxID: 160842

Cluster

View cluster (66 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 10-197
PDB
Domain cluster: rep: P3__YP_009509100__Daphne_virus_Y__282712__D3-191
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF13608.11 best Potyvirid-P3 95.7 4.90e-27 93.6% 35.4%
D2 medium residues 297-351
PDB
Domain cluster: rep: P3_protein__YP_001816828__Telosma_mosaic_virus__400394__D286-347
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2nr7A00 1.20.141.10 Mainly Alpha › Up-down Bundle › Chitosanase, subunit A; domain 1 › Chitosanase, subunit A, domain 1 0.83 68.0 4.48e-01 92.7% 24.7%
3elkA00 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 0.79 59.0 4.67e-01 90.9% 41.0%
2eucA00 1.10.8.570 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Hypothetical protein YfmB 0.76 65.0 5.21e-01 96.4% 51.4%
7r97A01 1.10.1520.10 Mainly Alpha › Orthogonal Bundle › Ribonuclease iii, N-terminal Endonuclease Domain; Chain A › Ribonuclease III domain 0.73 55.0 4.03e-01 81.8% 30.4%
2qvwA04 1.10.1520.10 Mainly Alpha › Orthogonal Bundle › Ribonuclease iii, N-terminal Endonuclease Domain; Chain A › Ribonuclease III domain 0.73 55.0 4.03e-01 81.8% 31.7%
3rv0C02 1.10.1520.10 Mainly Alpha › Orthogonal Bundle › Ribonuclease iii, N-terminal Endonuclease Domain; Chain A › Ribonuclease III domain 0.72 55.0 4.02e-01 81.8% 31.2%
3b0dB00 1.10.20.10 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A 0.70 60.0 5.02e-01 96.4% 66.3%
1rypA00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.69 58.0 3.81e-01 96.4% 58.4%
8f66A01 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.69 60.0 3.98e-01 96.4% 43.8%
6muwB00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.68 59.0 3.87e-01 96.4% 36.7%
1gvfB00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.68 53.0 3.37e-01 85.5% 23.3%
5fmgF00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.67 59.0 3.92e-01 98.2% 38.4%
2kn6A02 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.65 50.0 4.40e-01 83.6% 95.1%
4ixjA02 3.30.1690.20 Alpha Beta › 2-Layer Sandwich › TcpA-like pilin › 0.65 57.0 4.18e-01 98.2% 78.2%
3vm9A02 6.10.140.2110 Special › Helix non-globular › Helix Hairpins › 0.64 44.0 4.41e-01 90.9% 68.4%
4h63H01 1.20.58.1710 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.64 55.0 5.00e-01 92.7% 76.4%
3u9rB02 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.64 50.0 3.23e-01 87.3% 42.6%
2q00B00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.64 54.0 4.25e-01 96.4% 62.3%
6ofuA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.63 48.0 3.12e-01 83.6% 35.1%
3wfwA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.60 42.0 3.24e-01 80.0% 30.4%
2v8pA01 3.30.230.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.59 50.0 3.70e-01 98.2% 94.2%
4z4qA04 1.10.268.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase; domain 3 › Topoisomerase, domain 3 0.59 45.0 3.96e-01 87.3% 59.6%
1l1lA01 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.59 52.0 2.99e-01 98.2% 25.0%
2cr7A01 1.20.1160.11 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › Paired amphipathic helix 0.58 44.0 4.28e-01 85.5% 92.1%
3qdkB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.56 45.0 2.92e-01 90.9% 46.3%
2mw8A00 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.56 41.0 3.90e-01 94.5% 65.7%
4toiA02 1.10.287.610 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.55 44.0 4.64e-01 92.7% 100.0%
1chuA03 1.20.58.100 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Fumarate reductase/succinate dehydrogenase flavoprotein-like, C-terminal domain 0.55 46.0 4.03e-01 96.4% 71.6%
1ihuA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 42.0 2.84e-01 100.0% 71.4%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5063967 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.83 67.0 6.47e-01 94.5% 78.3%
None — 0.83 66.0 4.69e-01 94.5% 31.3%
3973557 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.82 66.0 5.13e-01 85.5% 47.3%
2807554 101.1.1.27 ↗ alpha arrays › HTH › HTH › Three-helical HTH › DsrC 0.82 65.0 5.20e-01 85.5% 45.6%
5067843 101.35.1.0 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.80 58.0 6.05e-01 81.8% 84.0%
3971933 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.77 62.0 5.89e-01 90.9% 73.8%
4452303 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.77 59.0 5.63e-01 90.9% 70.8%
3881313 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.77 54.0 5.11e-01 83.6% 63.1%
3690556 148.1.1.0 ↗ alpha arrays › Histone-like › Histone-related › Histone 0.76 56.0 5.43e-01 83.6% 71.7%
4555675 101.1.1.27 ↗ alpha arrays › HTH › HTH › Three-helical HTH › DsrC 0.75 58.0 4.68e-01 85.5% 44.0%
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) 0.75 63.0 6.03e-01 96.4% 95.4%
3329805 101.1.1.30 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3,Sigma70_r4 0.75 60.0 4.26e-01 90.9% 30.0%
3347305 101.1.1.30 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3,Sigma70_r4 0.74 59.0 4.19e-01 90.9% 29.1%
4550123 101.1.1.29 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3 0.74 56.0 5.51e-01 90.9% 75.0%
4148139 101.1.1.30 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3,Sigma70_r4 0.74 56.0 4.02e-01 90.9% 29.0%
3611998 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.73 56.0 5.40e-01 85.5% 81.5%
3644937 101.1.1.30 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3,Sigma70_r4 0.73 58.0 4.11e-01 89.1% 29.4%
3978620 101.1.1.30 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3,Sigma70_r4 0.73 56.0 3.94e-01 90.9% 27.3%
4339699 101.1.1.29 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3 0.73 56.0 5.69e-01 94.5% 83.6%
3948820 101.1.1.29 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3 0.73 55.0 4.69e-01 90.9% 50.0%
4056602 101.1.1.30 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3,Sigma70_r4 0.73 58.0 4.05e-01 90.9% 27.4%
5014864 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.73 57.0 4.68e-01 87.3% 51.0%
4946450 101.1.17.0 ↗ alpha arrays › HTH › HTH › FF domain 0.73 58.0 4.99e-01 89.1% 61.4%
3492370 4010.1.1.2 ↗ a+b complex topology › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › N-terminal domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_1,RNA_pol_Rpb2_3 0.72 54.0 3.39e-01 87.3% 15.3%
3936891 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.71 58.0 4.84e-01 90.9% 55.8%
3259657 605.8.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › BAS1536-like › BAS1536-like 0.69 58.0 5.34e-01 92.7% 81.4%
3477235 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.68 49.0 4.07e-01 83.6% 43.0%
4562263 3435.1.1.1 ↗ a+b two layers › Recombination-associated protein rdgC › Recombination-associated protein rdgC › Recombination-associated protein rdgC › RdgC 0.67 46.0 2.89e-01 80.0% 13.2%
3602986 5058.1.1.2 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › MS_channel_1st 0.66 53.0 4.37e-01 87.3% 51.6%
5027859 2498.1.1.0 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.65 49.0 3.68e-01 81.8% 32.6%
3188736 2003.1.1.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.63 46.0 3.17e-01 80.0% 35.5%
3941696 605.1.1.210 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › DUF997 0.63 53.0 5.01e-01 92.7% 84.6%
3953372 150.5.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › WXG100 0.61 52.0 4.30e-01 94.5% 54.1%
5039745 2003.1.1.36 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › 3HCDH_N 0.57 50.0 3.27e-01 94.5% 30.7%
3599791 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.56 44.0 2.79e-01 96.4% 15.0%
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 0.53 40.0 3.97e-01 90.9% 85.0%