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P3_protein

Euk-Vir

Tomato_necrotic_stunt_virus

P3_protein__YP_006280733__Tomato_necrotic_stunt_virus__1176153

Identity

Accession:
YP_006280733 ↗
Protein ID:
P3_protein
Kingdom:
euk

Quality

77.7 mean pLDDT

Taxonomy

Orthornavirae› Pisuviricota› Stelpaviricetes› Patatavirales› Potyviridae› Potyvirus› Tomato_necrotic_stunt_virus

TaxID: 1176153

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 11-221
PDB
Domain cluster: rep: P3__YP_009509100__Daphne_virus_Y__282712__D3-191
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF13608.11 best Potyvirid-P3 129.5 2.80e-37 85.8% 34.1%
D2 medium residues 227-301
PDB
Domain cluster: representative
D3 medium residues 302-374
PDB
Domain cluster: rep: third_protein__YP_008320584__Habenaria_mosaic_virus__1324128__D254-348
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2r6aC01 1.10.860.10 Mainly Alpha › Orthogonal Bundle › DNAb Helicase; Chain A › DNAb Helicase; Chain A 0.80 51.0 4.67e-01 71.2% 50.0%
2nr7A00 1.20.141.10 Mainly Alpha › Up-down Bundle › Chitosanase, subunit A; domain 1 › Chitosanase, subunit A, domain 1 0.79 59.0 4.24e-01 84.9% 29.4%
1txuA02 1.20.1050.80 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › VPS9 domain 0.79 54.0 4.08e-01 71.2% 48.1%
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 0.77 50.0 5.61e-01 72.6% 86.0%
2eucA00 1.10.8.570 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Hypothetical protein YfmB 0.74 53.0 4.59e-01 74.0% 50.5%
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 0.74 48.0 5.26e-01 76.7% 84.2%
3v9rA00 1.10.20.10 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A 0.73 55.0 5.11e-01 82.2% 64.8%
2oxlA00 1.20.5.5260 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.73 50.0 5.36e-01 71.2% 100.0%
1bdp002 1.20.1060.10 Mainly Alpha › Up-down Bundle › Taq DNA Polymerase; Chain T, domain 4 › Taq DNA Polymerase; Chain T, domain 4 0.70 51.0 4.46e-01 76.7% 78.9%
2rvqC01 1.10.20.10 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A 0.69 48.0 4.78e-01 72.6% 73.7%
6vddA02 1.20.1060.10 Mainly Alpha › Up-down Bundle › Taq DNA Polymerase; Chain T, domain 4 › Taq DNA Polymerase; Chain T, domain 4 0.69 51.0 4.36e-01 78.1% 82.6%
2vkzA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.69 49.0 3.32e-01 78.1% 21.0%
2y39A00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.69 50.0 4.29e-01 75.3% 56.4%
6muwB00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.67 52.0 3.65e-01 83.6% 67.7%
2hqcA01 1.20.1640.10 Mainly Alpha › Up-down Bundle › Multidrug efflux transporter AcrB transmembrane fold › Multidrug efflux transporter AcrB transmembrane domain 0.66 53.0 3.91e-01 89.0% 83.2%
2p11A02 1.10.286.50 Mainly Alpha › Orthogonal Bundle › GTP Cyclohydrolase I; Chain A, domain 1 › 0.66 46.0 4.67e-01 76.7% 73.0%
6qm7J00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.64 54.0 3.95e-01 93.2% 71.1%
3d36B02 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.64 37.0 3.98e-01 83.6% 67.2%
6muwM00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.64 54.0 3.91e-01 94.5% 68.5%
2uv8A07 6.10.140.1410 Special › Helix non-globular › Helix Hairpins › 0.63 50.0 4.71e-01 83.6% 74.1%
6muwK00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.62 53.0 3.92e-01 95.9% 71.8%
2i7uA00 6.10.250.1010 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.62 42.0 4.56e-01 74.0% 83.9%
6e5bN00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.61 52.0 3.82e-01 94.5% 86.9%
4h63K00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.61 40.0 3.65e-01 84.9% 50.0%
1e91A00 1.20.1160.11 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › Paired amphipathic helix 0.60 41.0 3.92e-01 71.2% 88.2%
4fcyA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.60 45.0 4.40e-01 79.5% 74.4%
4z4qA04 1.10.268.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase; domain 3 › Topoisomerase, domain 3 0.58 42.0 3.93e-01 75.3% 64.0%
2ld7B00 1.20.1160.11 Mainly Alpha › Up-down Bundle › Paired amphipathic helix 2 (pah2 repeat) › Paired amphipathic helix 0.58 42.0 4.20e-01 76.7% 92.0%
2ahoB02 1.10.150.190 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Translation initiation factor 2; subunit 1; domain 2 0.57 42.0 3.95e-01 80.8% 68.1%
ECOD (51)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5063967 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.84 55.0 5.99e-01 80.8% 81.7%
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 0.83 60.0 4.52e-01 80.8% 34.8%
3428775 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.82 60.0 3.80e-01 80.8% 17.5%
3662896 101.1.1.411 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r2 0.82 60.0 4.88e-01 80.8% 44.0%
3459967 142.1.1.0 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors 0.82 59.0 4.95e-01 80.8% 46.6%
3668668 101.1.1.29 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3 0.82 59.0 4.85e-01 80.8% 44.0%
4452096 142.1.1.1 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › Sigma70_r1_2,Sigma70_r2 0.82 62.0 4.41e-01 79.5% 50.8%
None — 0.81 59.0 4.53e-01 80.8% 36.7%
4452303 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.80 52.0 5.48e-01 71.2% 73.8%
5070203 109.4.1.202 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_16 0.79 67.0 4.08e-01 89.0% 23.2%
4550123 101.1.1.29 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3 0.78 51.0 5.56e-01 76.7% 81.7%
4339699 101.1.1.29 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3 0.77 51.0 5.76e-01 76.7% 89.1%
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) 0.77 57.0 5.99e-01 78.1% 100.0%
4518420 101.1.1.29 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3 0.77 50.0 5.28e-01 74.0% 75.4%
4131842 101.1.3.25 ↗ alpha arrays › HTH › HTH › tetra-helical, LuxR-like › Sigma70_r3 0.75 51.0 5.08e-01 79.5% 68.0%
4253264 101.1.1.29 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3 0.75 51.0 5.08e-01 79.5% 68.0%
3831185 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.74 47.0 4.82e-01 78.1% 67.1%
4876273 101.1.1.29 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3 0.73 45.0 4.76e-01 74.0% 68.7%
3705510 5076.1.1.0 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Mitochondrial ADP/ATP carrier › Mitochondrial ADP/ATP carrier 0.71 62.0 4.47e-01 95.9% 51.7%
4029754 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.71 55.0 5.22e-01 82.2% 89.4%
3688424 2003.1.5.79 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_23 0.69 54.0 3.57e-01 83.6% 84.7%
4978695 1075.1.2.0 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain 0.68 56.0 4.08e-01 89.0% 64.1%
4018473 5043.2.1.0 ↗ extended segments › Sensor proteins transmembrane domains › NarQ transmembrane domain › NarQ transmembrane domain 0.68 49.0 3.82e-01 84.9% 36.7%
3644937 101.1.1.30 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3,Sigma70_r4 0.67 52.0 3.98e-01 82.2% 45.6%
4086835 101.1.1.29 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3 0.67 53.0 5.13e-01 83.6% 92.5%
4233279 142.1.1.0 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors 0.67 51.0 3.50e-01 80.8% 32.5%
5054860 3755.3.1.305 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › Rad50_zn_hook 0.66 51.0 3.86e-01 84.9% 93.0%
4238054 142.1.1.0 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors 0.66 51.0 3.49e-01 82.2% 31.0%
4964254 4333.1.1.0 ↗ a+b complex topology › DNA methylase specificity domain › DNA methylase specificity domain › DNA methylase specificity domain 0.65 49.0 3.37e-01 80.8% 32.7%
3948820 101.1.1.29 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3 0.65 50.0 4.72e-01 83.6% 84.4%
4056602 101.1.1.30 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3,Sigma70_r4 0.65 52.0 3.85e-01 84.9% 98.3%
3729389 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.64 52.0 3.95e-01 84.9% 40.6%
4940618 198.1.1.0 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.64 49.0 4.77e-01 80.8% 75.0%
4388780 101.1.1.30 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3,Sigma70_r4 0.63 51.0 4.01e-01 86.3% 53.1%
3826046 101.1.1.30 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3,Sigma70_r4 0.63 47.0 3.68e-01 82.2% 42.4%
3329805 101.1.1.30 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3,Sigma70_r4 0.62 50.0 3.86e-01 86.3% 47.5%
4253265 101.1.1.30 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3,Sigma70_r4 0.62 50.0 3.80e-01 86.3% 46.7%
3980765 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.62 50.0 3.80e-01 86.3% 46.7%
4148139 101.1.1.30 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3,Sigma70_r4 0.62 50.0 3.87e-01 86.3% 49.0%
3429968 101.1.1.29 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3 0.60 44.0 4.50e-01 80.8% 82.9%
3288971 101.1.1.30 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3,Sigma70_r4 0.60 47.0 3.76e-01 86.3% 53.3%
3303765 101.1.1.30 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3,Sigma70_r4 0.60 48.0 3.68e-01 86.3% 48.1%
3839135 2004.1.1.76 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF87 0.59 46.0 2.96e-01 87.7% 30.0%
3284461 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.59 46.0 3.21e-01 86.3% 32.0%
3280723 101.1.1.29 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3 0.59 46.0 4.37e-01 87.7% 88.9%
None — 0.58 46.0 3.20e-01 86.3% 32.2%
3599791 219.1.1.3 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH 0.56 40.0 2.65e-01 78.1% 15.8%
3170329 604.12.1.9 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › ATG1-like_MIT2 0.54 41.0 3.60e-01 80.8% 90.0%
3373039 192.17.1.0 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.54 38.0 3.31e-01 75.3% 64.3%
3222692 7525.1.1.2 ↗ a/b three-layered sandwiches › Phosphoglycerate mutase-like › Phosphoglycerate mutase-like › Phosphoglycerate mutase-like › His_Phos_2 0.53 44.0 2.86e-01 90.4% 24.9%
4009355 206.1.3.5 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › DNA_ligase_aden 0.50 42.0 2.81e-01 91.8% 95.9%