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P_protein

Euk-Vir

Lettuce_yellow_mottle_virus

P_protein__YP_002308372__Lettuce_yellow_mottle_virus__471285

Identity

Accession:
YP_002308372 ↗
Protein ID:
P_protein
Kingdom:
euk

Quality

69.2 mean pLDDT

Cluster

View cluster (3 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 60-175
PDB
Domain cluster: representative
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2q12A00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.78 55.0 4.25e-01 87.9% 34.7%
4wpeA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.69 58.0 4.31e-01 88.8% 38.9%
2v0oB00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.69 58.0 4.33e-01 90.5% 38.4%
3okqA00 1.20.58.1540 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Actin interacting protein 3, C-terminal domain 0.68 51.0 5.01e-01 90.5% 72.8%
ECOD (6)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3710351 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.77 61.0 5.23e-01 82.8% 77.1%
3920125 3755.3.1.450 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › Uso1_p115_C 0.75 60.0 4.92e-01 87.9% 49.7%
4950969 2004.1.1.87 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N 0.70 54.0 3.54e-01 91.4% 20.0%
3726923 3291.1.1.1 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Snf7 0.70 47.0 4.54e-01 75.0% 60.8%
3470739 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.69 59.0 4.73e-01 91.4% 60.0%
3889810 4177.1.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.67 54.0 4.22e-01 84.5% 51.1%
D2 high residues 235-305
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF21658.3 best LNYV_PP_C 130.0 3.60e-38 84.5% 100.0%
CATH (35)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3t4rA00 1.20.120.1590 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.96 91.0 9.07e-01 98.6% 97.2%
1rfyB00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.74 41.0 3.76e-01 94.4% 44.3%
4a15A03 1.10.275.40 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › 0.70 52.0 4.16e-01 78.9% 67.9%
2gf4A00 1.20.1270.110 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Uncharacterised protein family UPF0058 0.68 53.0 4.93e-01 84.5% 73.9%
1b5lA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.67 58.0 4.55e-01 95.8% 58.6%
1on2A02 1.10.60.10 Mainly Alpha › Orthogonal Bundle › Diphtheria Toxin Repressor; domain 2 › Iron dependent repressor, metal binding and dimerisation domain 0.67 46.0 4.86e-01 71.8% 90.5%
7s0rB01 1.20.81.20 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › 0.67 54.0 5.35e-01 87.3% 89.5%
1oksA00 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.65 46.0 5.21e-01 78.9% 98.1%
2wl8C00 1.20.120.900 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Pex19, mPTS binding domain 0.65 49.0 4.21e-01 78.9% 78.0%
3fxdB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.64 38.0 4.23e-01 91.5% 74.1%
2p5tA00 1.10.8.130 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.64 52.0 4.77e-01 88.7% 87.0%
2qffA00 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.63 48.0 4.80e-01 81.7% 89.2%
8d7hD01 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.62 52.0 3.92e-01 93.0% 50.3%
1r9dA01 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.61 44.0 2.51e-01 88.7% 6.9%
4am8E01 3.40.50.1370 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Aspartate/ornithine carbamoyltransferase 0.60 51.0 3.90e-01 94.4% 71.9%
2oo2A00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.59 46.0 4.54e-01 84.5% 88.2%
4mcwA02 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.58 42.0 3.09e-01 76.1% 78.8%
1k32A03 3.30.750.44 Alpha Beta › 2-Layer Sandwich › Transcription Regulator spoIIAA › 0.58 43.0 4.31e-01 80.3% 80.6%
1xrhD01 1.10.1530.10 Mainly Alpha › Orthogonal Bundle › Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 › Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel 0.58 42.0 3.74e-01 77.5% 92.2%
1f68A00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.58 44.0 3.96e-01 84.5% 72.8%
3t38A01 1.10.8.1060 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Corynebacterium glutamicum thioredoxin-dependent arsenate reductase, N-terminal domain 0.57 47.0 4.71e-01 91.5% 93.0%
1dqeA00 1.10.238.20 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain 0.57 44.0 3.56e-01 90.1% 43.1%
2q00B00 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.56 45.0 3.80e-01 88.7% 94.3%
2p0tA01 1.10.60.30 Mainly Alpha › Orthogonal Bundle › Diphtheria Toxin Repressor; domain 2 › PSPTO4464-like domains 0.56 41.0 4.01e-01 77.5% 72.4%
2gscC00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.56 49.0 4.26e-01 98.6% 71.8%
3gdeA01 1.10.3260.10 Mainly Alpha › Orthogonal Bundle › DNA ligase i, domain 1 › DNA ligase, ATP-dependent, N-terminal domain 0.56 37.0 2.70e-01 88.7% 22.3%
1q0gA00 1.20.120.400 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nickel-containing superoxide dismutase 0.54 41.0 3.60e-01 84.5% 60.7%
4pdyA02 3.90.1200.10 Alpha Beta › Alpha-Beta Complex › Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 › Aminoglycoside phosphotransferase (APH), C-terminal lobe 0.54 43.0 3.11e-01 90.1% 82.4%
7dd0C01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 42.0 3.08e-01 91.5% 38.4%
1v9mA03 1.20.1690.10 Mainly Alpha › Up-down Bundle › V-type ATP synthase subunit C fold › V-type ATP synthase subunit C domain 0.54 44.0 4.01e-01 90.1% 91.7%
2v0oB00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.53 44.0 3.02e-01 94.4% 73.8%
2ivxB01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.53 43.0 3.61e-01 95.8% 80.7%
2yksA02 1.20.58.390 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Neurotransmitter-gated ion-channel transmembrane domain 0.52 41.0 3.60e-01 90.1% 83.8%
3tuiD01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 39.0 2.84e-01 84.5% 40.5%
3nc3B00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.51 46.0 2.89e-01 100.0% 22.9%
ECOD (38)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
185545 3571.1.1.1 ↗ alpha arrays › Lettuce necrotic yellow virus phosphoprotein C-terminal domain › Lettuce necrotic yellow virus phosphoprotein C-terminal domain › Lettuce necrotic yellow virus phosphoprotein C-terminal domain › LNYV_PP_C 0.96 91.0 9.07e-01 98.6% 97.2%
4116972 375.1.9.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Zinc-nucleated domain of serine integrase 0.80 45.0 4.01e-01 78.9% 42.1%
3975777 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.72 44.0 3.92e-01 80.3% 45.3%
3693574 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.69 59.0 5.70e-01 100.0% 85.0%
4096686 632.7.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain 0.65 52.0 4.96e-01 87.3% 88.2%
4949658 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.64 51.0 4.94e-01 85.9% 93.8%
5060252 632.23.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Helical linker domain in nicking endonuclease N.BspD6I › Helical linker domain in nicking endonuclease N.BspD6I 0.64 51.0 4.87e-01 87.3% 84.7%
5031855 632.15.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) 0.64 51.0 4.95e-01 87.3% 95.0%
4352674 632.1.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.63 52.0 4.53e-01 90.1% 78.1%
4928025 1111.1.1.1 ↗ alpha complex topology › Trimeric intracellular cation (TRIC) channel › Trimeric intracellular cation (TRIC) channel › Trimeric intracellular cation (TRIC) channel › Gly_transporter 0.62 52.0 3.84e-01 94.4% 40.0%
5050851 601.7.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.62 48.0 3.93e-01 83.1% 67.7%
4420734 5065.1.1.2 ↗ alpha bundles › Type II ABC importer transmembrane domain fold › Type II ABC importer transmembrane domain fold › Type II ABC importer transmembrane domain fold › FecCD 0.61 55.0 3.55e-01 98.6% 69.3%
3335328 103.4.1.0 ↗ alpha arrays › RuvA-C › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein 0.61 54.0 4.83e-01 98.6% 84.0%
4471275 5065.1.1.2 ↗ alpha bundles › Type II ABC importer transmembrane domain fold › Type II ABC importer transmembrane domain fold › Type II ABC importer transmembrane domain fold › FecCD 0.61 54.0 3.53e-01 98.6% 71.6%
3420431 632.7.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain 0.60 48.0 4.54e-01 85.9% 78.8%
3504477 1111.1.1.1 ↗ alpha complex topology › Trimeric intracellular cation (TRIC) channel › Trimeric intracellular cation (TRIC) channel › Trimeric intracellular cation (TRIC) channel › Gly_transporter 0.60 52.0 3.77e-01 95.8% 38.5%
3617518 632.15.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) 0.60 43.0 4.41e-01 77.5% 82.9%
4937420 2004.1.1.42 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE 0.60 41.0 2.51e-01 73.2% 14.5%
3949864 632.1.1.37 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain › DUF6474 0.59 47.0 4.43e-01 88.7% 91.1%
3280911 5069.1.3.58 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits › DoxX 0.59 39.0 3.74e-01 100.0% 57.6%
1144175 632.2.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › FIVAR 0.58 41.0 4.28e-01 74.6% 93.9%
5053570 148.1.3.411 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › HAAS 0.56 43.0 4.27e-01 87.3% 100.0%
3563894 59.1.4.2 ↗ beta complex topology › triple barrel › triple barrel › TFIID subunits TAF1-TAF7 › DUF3591 0.56 49.0 3.00e-01 98.6% 90.5%
3262801 3788.1.1.0 ↗ alpha bundles › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) 0.55 43.0 3.56e-01 84.5% 53.6%
3495102 4106.1.1.1 ↗ few secondary structure elements › Zinc hairpin stack › Zinc hairpin stack › Zinc hairpin stack › DHHC 0.54 42.0 3.06e-01 85.9% 64.7%
4258320 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 0.54 44.0 4.26e-01 88.7% 81.2%
5044944 223.1.1.13 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_3 0.54 37.0 3.16e-01 73.2% 78.4%
3430911 142.1.1.0 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors 0.53 43.0 4.18e-01 95.8% 98.8%
4977214 2004.1.1.308 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_21 0.53 40.0 3.28e-01 85.9% 61.3%
None — 0.53 40.0 2.44e-01 87.3% 15.5%
3875578 2004.1.1.417 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran, AAA_21 0.53 41.0 2.82e-01 90.1% 30.5%
4946942 102.1.1.0 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like 0.53 31.0 2.80e-01 81.7% 37.5%
3940138 2004.1.1.417 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran, AAA_21 0.52 39.0 2.41e-01 87.3% 15.8%
5039200 2004.1.1.5 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.52 39.0 2.84e-01 87.3% 37.9%
4949062 2004.1.1.5 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.52 38.0 2.89e-01 83.1% 44.9%
3268622 604.12.1.1 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › MIT 0.52 44.0 3.84e-01 91.5% 65.7%
4944262 2004.1.1.5 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.52 39.0 2.69e-01 84.5% 33.3%
3402262 2004.1.1.5 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.51 39.0 2.84e-01 90.1% 35.8%