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P3_protein

Euk-Vir

Onion_yellow_dwarf_virus

P3_protein__NP_871740__Onion_yellow_dwarf_virus__43130

Identity

Accession:: NP_871740 ↗
Protein ID:: P3_protein
Kingdom:: euk

Quality

62.1 mean pLDDT

Taxonomy

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

TaxID: 43130

Cluster

Singleton — not in a non-trivial cluster

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 high residues 170-352

PDB

Domain cluster: rep: P3__YP_009509100__Daphne_virus_Y__282712__D3-191

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF13608.11 best	Potyvirid-P3	56.6	3.50e-15	84.2%	33.9%

CATH (13)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2i6hA02	1.25.40.10	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain	0.62	32.0	4.17e-01	79.2%	90.6%
5ffdA00	1.20.1260.10	Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle	0.55	32.0	3.69e-01	82.5%	76.6%
2rldA00	1.20.1440.60	Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence	0.53	33.0	4.03e-01	89.6%	100.0%
2h7oA01	1.20.120.1330	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Rac1-binding domain, N-terminal GTPase binding subdomain	0.53	29.0	3.49e-01	80.9%	78.9%
1yo7A00	1.20.120.230	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like	0.53	34.0	4.07e-01	86.9%	98.3%
3p5nA00	1.10.1760.20	Mainly Alpha › Orthogonal Bundle › Arp2/3 complex 21 kDa subunit ARPC3 ›	0.52	40.0	4.23e-01	80.9%	97.0%
4djhA01	1.20.1070.10	Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins	0.52	45.0	3.91e-01	94.5%	90.6%
3kwoA00	1.20.1260.10	Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle	0.52	33.0	3.57e-01	85.2%	75.8%
4ib4A01	1.20.1070.10	Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins	0.52	45.0	3.95e-01	96.2%	89.5%
3efzB00	1.20.190.20	Mainly Alpha › Up-down Bundle › Delta-Endotoxin; domain 1 › 14-3-3 domain	0.51	39.0	3.68e-01	79.2%	99.6%
8hixR01	1.20.1070.10	Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins	0.51	44.0	3.87e-01	94.5%	90.0%
3fseB02	1.20.1260.10	Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle	0.50	31.0	3.43e-01	82.5%	75.0%
5nnpE01	1.25.40.1040	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ›	0.50	38.0	2.81e-01	77.6%	47.0%

ECOD (11)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3830380	6155.1.1.1 ↗	alpha duplicates or obligate multimers › TOG superfamily › SWEET transporter › SWEET transporter › MtN3_slv	0.66	31.0	3.66e-01	95.6%	61.5%
3188566	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.60	44.0	4.05e-01	74.9%	82.6%
4932048	3543.1.1.0 ↗	alpha complex topology › Acid-activated urea channel › Acid-activated urea channel › Acid-activated urea channel	0.59	44.0	4.48e-01	76.0%	86.7%
4201685	174.1.1.0 ↗	few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain	0.57	34.0	4.08e-01	90.2%	89.2%
3263292	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.56	33.0	3.97e-01	92.9%	87.5%
5004350	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.55	44.0	3.29e-01	84.2%	83.5%
3557924	109.4.1.1300 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_8, TPR_16, TPR_19	0.53	43.0	3.10e-01	85.2%	45.2%
3196650	109.57.1.1 ↗	alpha superhelices › Repetitive alpha hairpins › Sterol regulatory element-binding protein 1 (Sre1) C-terminal domain › Sterol regulatory element-binding protein 1 (Sre1) C-terminal domain › DUF2014	0.53	40.0	3.53e-01	78.1%	54.8%
4975978	109.4.1.198 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_12	0.53	39.0	3.55e-01	76.0%	78.0%
3587256	633.22.1.0 ↗	alpha bundles › Bromodomain-like › Vitamin K epoxide reductase (VKOR) › Vitamin K epoxide reductase (VKOR)	0.51	35.0	3.51e-01	90.7%	66.5%
3625427	174.1.1.0 ↗	few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain	0.50	32.0	3.86e-01	89.1%	100.0%

D2 high residues 448-528

PDB

Domain cluster: rep: third_protein__YP_008320584__Habenaria_mosaic_virus__1324128__D254-348

CATH (13)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4oydB00	1.10.132.20	Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor	0.74	55.0	4.79e-01	82.7%	53.0%
2nr7A00	1.20.141.10	Mainly Alpha › Up-down Bundle › Chitosanase, subunit A; domain 1 › Chitosanase, subunit A, domain 1	0.74	51.0	3.83e-01	74.1%	29.9%
3v9rA00	1.10.20.10	Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A	0.72	50.0	4.88e-01	75.3%	65.9%
2y39A00	1.20.120.1490	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) ›	0.67	49.0	4.39e-01	86.4%	55.5%
2bdeA03	1.20.58.1160	Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 ›	0.66	43.0	4.41e-01	90.1%	70.1%
3nyjA00	1.20.120.770	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Amyloid precursor protein, E2 domain	0.65	58.0	4.49e-01	100.0%	60.2%
3a8pA02	6.10.140.680	Special › Helix non-globular › Helix Hairpins ›	0.65	53.0	4.66e-01	86.4%	61.4%
2rd0B00	1.10.287.1490	Mainly Alpha › Orthogonal Bundle › Helix Hairpins ›	0.64	54.0	4.54e-01	97.5%	54.0%
4mndA02	1.20.120.1760	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CDP-alcohol phosphotransferase transmembrane (TM) domain	0.57	34.0	2.68e-01	80.2%	25.1%
3wfwA00	1.10.490.10	Mainly Alpha › Orthogonal Bundle › Globin-like › Globins	0.56	45.0	3.84e-01	90.1%	62.3%
4qgpB00	1.10.287.1080	Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like	0.53	39.0	3.61e-01	77.8%	68.2%
1kqpA00	3.40.50.620	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs	0.51	38.0	2.68e-01	80.2%	45.8%
3frwB00	1.10.1270.10	Mainly Alpha › Orthogonal Bundle › Trp Operon Repressor; Chain A › TrpR-like	0.51	33.0	3.19e-01	79.0%	56.2%

ECOD (18)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
5063967	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.82	49.0	5.62e-01	70.4%	81.7%
4993207	3755.3.1.0 ↗	alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin	0.81	63.0	5.18e-01	88.9%	47.9%
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	0.80	59.0	5.79e-01	77.8%	72.9%
3802520	101.1.1.476 ↗	alpha arrays › HTH › HTH › Three-helical HTH › POX	0.79	53.0	4.90e-01	81.5%	56.0%
3662896	101.1.1.411 ↗	alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r2	0.75	54.0	4.55e-01	76.5%	48.0%
4016091	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	0.73	55.0	5.48e-01	80.2%	76.5%
3654904	3755.4.1.17 ↗	alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Rx_N	0.73	54.0	4.46e-01	90.1%	45.0%
4518420	101.1.1.29 ↗	alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3	0.69	47.0	5.23e-01	70.4%	96.9%
3294780	3755.3.1.375 ↗	alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › DUF4079	0.66	58.0	4.72e-01	97.5%	54.0%
4940618	198.1.1.0 ↗	alpha arrays › Saposin-like › Saposin-like › Saposin-like	0.64	45.0	4.61e-01	72.8%	75.0%
5077194	191.1.1.0 ↗	alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain	0.64	40.0	3.50e-01	70.4%	42.9%
4228483	192.15.1.46 ↗	alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › Ribophorin_II_C	0.63	40.0	3.59e-01	70.4%	46.4%
3938092	3911.1.1.0 ↗	extended segments › Exosome complex protein LRP1 › Exosome complex protein LRP1 › Exosome complex protein LRP1	0.63	49.0	4.36e-01	81.5%	70.0%
5039745	2003.1.1.36 ↗	a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › 3HCDH_N	0.62	45.0	3.28e-01	80.2%	27.6%
4010395	622.4.1.26 ↗	alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related › HisKA	0.62	46.0	4.92e-01	79.0%	92.9%
3599791	219.1.1.3 ↗	a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › UCH	0.59	40.0	2.63e-01	70.4%	15.8%
3407923	192.24.1.1 ↗	alpha bundles › Long alpha-hairpin › RPC62 helical hairpin domain › RPC62 helical hairpin domain › RPC3_helical	0.58	44.0	4.13e-01	80.2%	85.0%
3329805	101.1.1.30 ↗	alpha arrays › HTH › HTH › Three-helical HTH › Sigma70_r3,Sigma70_r4	0.58	44.0	3.58e-01	82.7%	55.6%

D3 medium residues 353-403

PDB