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papain-like_protease

Euk-Vir

Bean_yellow_disorder_virus

papain-like_protease__YP_001816797__Bean_yellow_disorder_virus__267970

Identity

Accession:
YP_001816797 ↗
Protein ID:
papain-like_protease
Kingdom:
euk

Quality

68.0 mean pLDDT

Taxonomy

Orthornavirae› Kitrinoviricota› Alsuviricetes› Martellivirales› Closteroviridae› Crinivirus› Bean_yellow_disorder_virus

TaxID: 267970

Cluster

View cluster (2 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 171-308
PDB
Domain cluster: representative
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3d2lA02 2.20.25.110 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › S-adenosyl-L-methionine-dependent methyltransferases 0.72 30.0 4.38e-01 89.9% 85.7%
3bxoA02 2.20.130.10 Mainly Beta › Single Sheet › S-adenosyl-L-methionine-dependent methyltransferases › CAC2371-like domains 0.66 27.0 4.11e-01 90.6% 89.8%
4aeeA05 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.64 28.0 3.90e-01 95.7% 83.6%
3exmA01 2.40.380.10 Mainly Beta › Beta Barrel › FomD barrel-like fold › FomD-like 0.60 45.0 3.98e-01 78.3% 84.1%
1ospO01 2.40.128.160 Mainly Beta › Beta Barrel › Lipocalin › C1 set domains (antibody constant domain-like) 0.60 34.0 3.80e-01 99.3% 71.4%
6ka3A01 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.59 41.0 4.01e-01 81.2% 66.0%
4xb3A03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.58 29.0 3.92e-01 94.9% 91.7%
3tzgA00 2.40.160.150 Mainly Beta › Beta Barrel › Porin › 0.57 46.0 3.85e-01 86.2% 79.1%
4ge1C00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.57 46.0 4.16e-01 87.7% 77.2%
3eliA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.56 41.0 4.09e-01 76.1% 81.9%
1xuvA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.56 41.0 3.93e-01 76.1% 74.8%
4iglB00 2.180.10.10 Mainly Beta › Shell › RHS repeat-associated core › RHS repeat-associated core 0.55 45.0 2.92e-01 87.7% 85.3%
3dtdD00 2.60.40.1880 Mainly Beta › Sandwich › Immunoglobulin-like › Invasion associated locus B (IalB) protein 0.54 41.0 4.03e-01 79.0% 95.9%
2lpuA00 3.30.1460.50 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.53 36.0 3.58e-01 99.3% 64.2%
6igbA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.53 39.0 2.85e-01 75.4% 50.1%
1nbwA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.53 34.0 3.49e-01 79.0% 66.7%
4xmeA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.52 42.0 3.88e-01 87.0% 78.8%
5gv0A00 2.40.160.110 Mainly Beta › Beta Barrel › Porin › 0.52 41.0 3.92e-01 83.3% 93.2%
2i99A01 3.30.1780.10 Alpha Beta › 2-Layer Sandwich › ornithine cyclodeaminase, domain 1 › ornithine cyclodeaminase, domain 1 0.52 42.0 4.10e-01 95.7% 78.7%
7knlA01 2.40.128.30 Mainly Beta › Beta Barrel › Lipocalin › Avidin-like 0.51 36.0 3.89e-01 91.3% 86.0%
2pwwA00 3.30.310.100 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › YugN-like 0.51 34.0 3.68e-01 77.5% 80.0%
ECOD (23)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5076458 331.3.1.9 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › AHSA1 0.60 38.0 3.82e-01 81.9% 62.1%
5056218 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.59 32.0 4.13e-01 73.2% 100.0%
4285338 5087.1.1.0 ↗ beta meanders › Lipovitellin-phosvitin complex › Lipovitellin LV-2 › Lipovitellin LV-2 0.59 44.0 3.94e-01 77.5% 90.5%
3426868 331.3.1.17 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › VASt 0.57 43.0 3.94e-01 81.2% 60.0%
1395707 5084.5.1.16 ↗ beta barrels › Outer membrane meander beta-barrels › Porins › Porin › BVU_2266-like 0.57 46.0 3.85e-01 86.2% 79.1%
5024957 7089.1.1.0 ↗ a+b two layers › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD › Methane monooxygenase hydroxylase, MmoD 0.57 33.0 4.23e-01 77.5% 100.0%
4928052 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 0.56 43.0 3.22e-01 80.4% 40.8%
3271533 331.4.1.0 ↗ a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 0.56 35.0 3.86e-01 78.3% 78.7%
3208973 4099.1.1.4 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › CENP-O 0.55 39.0 4.21e-01 94.2% 87.7%
4426077 241.1.1.2 ↗ a+b two layers › Type III secretory system chaperone-like › Type III secretory system chaperone › Type III secretory system chaperone › Autophagy_act_C 0.55 41.0 3.96e-01 100.0% 67.7%
3464885 331.3.1.1 ↗ a+b two layers › TBP-like › Bet v1-like › Bet v1-like › Bet_v_1 0.55 39.0 3.84e-01 81.2% 68.0%
865437 241.1.1.2 ↗ a+b two layers › Type III secretory system chaperone-like › Type III secretory system chaperone › Type III secretory system chaperone › Autophagy_act_C 0.55 38.0 3.68e-01 100.0% 63.6%
3328359 844.1.1.2 ↗ beta barrels › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › Transcriptional factor tubby, C-terminal domain › LOR 0.55 47.0 4.22e-01 93.5% 82.1%
4875038 9.1.1.11 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › Lipocalin_2 0.54 44.0 4.30e-01 87.7% 93.3%
4016866 4099.1.1.0 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.54 40.0 4.28e-01 94.2% 92.2%
3577548 331.12.1.0 ↗ a+b two layers › TBP-like › YugN-like › YugN-like 0.53 36.0 3.92e-01 77.5% 82.3%
3289783 11.1.1.600 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › RskA_C 0.53 32.0 3.55e-01 93.5% 76.2%
3488379 216.1.1.4 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › RWD 0.53 39.0 4.05e-01 97.1% 81.5%
5010078 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.53 44.0 3.24e-01 89.9% 54.7%
2448551 213.1.1.0 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.53 33.0 3.53e-01 73.9% 70.6%
3626881 5084.5.1.33 ↗ beta barrels › Outer membrane meander beta-barrels › Porins › Porin › DNAJC11_beta-barrel 0.53 40.0 3.17e-01 96.4% 37.6%
3445404 4210.1.1.0 ↗ a+b two layers › WGR domain › WGR domain › WGR domain 0.51 31.0 3.53e-01 87.7% 81.0%
3997433 2003.1.5.13 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Spermine_synth 0.51 46.0 3.73e-01 100.0% 81.9%
D2 high residues 371-504
PDB
Domain cluster: representative
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1gccA00 3.30.730.10 Alpha Beta › 2-Layer Sandwich › GCC-box Binding Domain › AP2/ERF domain 0.60 29.0 3.96e-01 87.3% 95.2%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3564972 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.70 24.0 3.31e-01 90.3% 58.6%
4119875 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.60 25.0 3.66e-01 72.4% 83.1%
4931822 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.57 23.0 3.11e-01 88.8% 70.8%
5075465 4325.1.1.0 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like 0.52 24.0 3.30e-01 90.3% 90.0%
D3 medium residues 83-157
PDB