←Back to structures

P1_protein

Euk-Vir

Saffron_latent_virus

P1_protein__YP_009458609__Saffron_latent_virus__2070152

Identity

Accession:
YP_009458609 ↗
Protein ID:
P1_protein
Kingdom:
euk

Quality

80.9 mean pLDDT

Taxonomy

Orthornavirae› Pisuviricota› Stelpaviricetes› Patatavirales› Potyviridae› Potyvirus› Saffron_latent_virus

TaxID: 2070152

Cluster

View cluster (16 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 187-316
PDB
Domain cluster: rep: P1__YP_006908980__Rose_yellow_mosaic_virus__1048434__D303-423
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01577.23 best Peptidase_S30 115.5 4.40e-33 100.0% 53.9%
D2 medium residues 57-130
PDB
Domain cluster: rep: P1_protein__YP_001974436__Fritillary_virus_Y__332471__D63-123
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3aeiA00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.68 37.0 3.38e-01 78.4% 41.5%
7kfuC02 1.20.120.920 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CRISPR-associated endonuclease Cas1, C-terminal domain 0.59 46.0 3.23e-01 85.1% 44.6%
1rsgA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.58 40.0 2.81e-01 73.0% 84.5%
1fthA00 3.90.470.20 Alpha Beta › Alpha-Beta Complex › Ribosomal Protein L22; Chain A › 4'-phosphopantetheinyl transferase domain 0.57 39.0 3.36e-01 70.3% 82.9%
2gqfA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.55 38.0 2.65e-01 71.6% 64.3%
7bqiA01 1.20.58.900 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › RUN domain 0.53 37.0 2.95e-01 73.0% 80.1%
1pqsA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.52 31.0 3.15e-01 75.7% 57.1%
2w00A02 3.90.640.50 Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › 0.52 30.0 3.07e-01 70.3% 54.8%
3hwcA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.51 36.0 2.62e-01 100.0% 26.2%
2fji101 1.10.357.50 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › 0.51 39.0 2.77e-01 87.8% 28.2%
6ketA01 3.20.20.30 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Luciferase-like domain 0.50 41.0 2.65e-01 89.2% 66.1%
ECOD (34)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3544534 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.76 36.0 3.54e-01 79.7% 42.5%
4115648 3671.1.1.1 ↗ alpha duplicates or obligate multimers › Translocated intimin receptor Tir extracellular domain › Translocated intimin receptor Tir extracellular domain › Translocated intimin receptor Tir extracellular domain › Tir_receptor_M 0.70 36.0 3.49e-01 79.7% 44.7%
3470595 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.69 37.0 2.68e-01 81.1% 20.0%
4023956 3871.1.1.1 ↗ alpha duplicates or obligate multimers › PHIST › PHIST › PHIST › PRESAN 0.68 40.0 3.32e-01 70.3% 33.8%
3716174 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.68 43.0 3.83e-01 95.9% 43.6%
4033043 616.1.1.41 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › Terminase_4 0.66 37.0 3.45e-01 70.3% 44.4%
3364027 101.1.2.245 ↗ alpha arrays › HTH › HTH › winged helix domain › PORR 0.65 45.0 3.27e-01 73.0% 47.9%
3287147 4177.1.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.63 39.0 2.95e-01 91.9% 27.6%
3931057 558.1.1.0 ↗ alpha duplicates or obligate multimers › Lis-homology dimerization domain › Lis-homology dimerization domain › Lis-homology dimerization domain 0.62 28.0 3.10e-01 75.7% 48.3%
3474413 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.62 37.0 2.35e-01 81.1% 11.9%
3509321 5054.1.1.0 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels 0.58 44.0 2.88e-01 83.8% 50.9%
3958549 2006.1.2.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › DHH phosphoesterases 0.57 38.0 3.03e-01 71.6% 31.2%
3926959 605.6.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › HP1531-like › HP1531-like 0.57 38.0 3.62e-01 75.7% 60.0%
4043003 601.7.1.6 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain › GlnD_UR_UTase 0.56 41.0 3.19e-01 78.4% 38.2%
3784236 807.1.1.0 ↗ a+b two layers › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) › Allophycocyanin linker chain (domain) 0.55 41.0 3.59e-01 78.4% 76.4%
3478703 192.29.1.24 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › TMEM237 0.55 45.0 3.28e-01 87.8% 78.5%
5049161 177.1.1.0 ↗ alpha bundles › Phospholipase C/P1 nuclease › Phospholipase C/P1 nuclease › Phospholipase C/P1 nuclease 0.55 35.0 2.67e-01 100.0% 23.3%
5000789 192.2.1.1 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.55 40.0 3.51e-01 82.4% 53.3%
4026519 3871.1.1.1 ↗ alpha duplicates or obligate multimers › PHIST › PHIST › PHIST › PRESAN 0.54 39.0 3.23e-01 75.7% 87.4%
None — 0.54 38.0 2.61e-01 73.0% 89.0%
3924318 6166.1.1.0 ↗ alpha bundles › N-terminal domain of Delta(14)-sterol reductase, MaSR1 › N-terminal domain of Delta(14)-sterol reductase, MaSR1 › N-terminal domain of Delta(14)-sterol reductase, MaSR1 0.53 36.0 2.62e-01 70.3% 73.3%
3587282 142.1.1.10 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors › HTH_16 0.52 28.0 2.91e-01 74.3% 54.3%
4410759 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.52 41.0 3.54e-01 85.1% 56.5%
3707907 320.4.1.3 ↗ a+b two layers › R3H domain-like › PUB domain › PUB domain › PUB 0.52 36.0 3.05e-01 71.6% 74.8%
3783976 192.2.1.2 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin 0.52 42.0 3.91e-01 86.5% 76.7%
3660366 2003.1.2.20 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › HI0933_like 0.51 37.0 2.44e-01 75.7% 25.7%
4960388 5048.1.1.2 ↗ alpha complex topology › Aquaporin-like › Aquaporin-like › Aquaporin-like › Form_Nir_trans 0.51 40.0 2.70e-01 86.5% 46.1%
3276546 314.1.1.9 ↗ a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › tRNA-synt_His 0.51 37.0 2.43e-01 77.0% 95.4%
4975047 2003.1.2.20 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › HI0933_like 0.51 36.0 2.41e-01 73.0% 31.8%
None — 0.51 36.0 2.45e-01 73.0% 35.2%
3589784 2003.6.1.5 ↗ a/b three-layered sandwiches › Rossmann-like › Ribokinase-like › Ribokinase-like › Phos_pyr_kin 0.51 42.0 2.88e-01 90.5% 71.5%
3939311 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.50 41.0 3.58e-01 87.8% 60.9%
3937632 859.1.1.0 ↗ a+b two layers › The spindle assembly checkpoint protein mad2 › The spindle assembly checkpoint protein mad2 › The spindle assembly checkpoint protein mad2 0.50 36.0 2.73e-01 75.7% 42.3%
None — 0.50 35.0 2.38e-01 74.3% 47.8%