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L2_capsid_protein

Euk-Vir

Caretta_caretta_papillomavirus_1

L2_capsid_protein__YP_002308362__Caretta_caretta_papillomavirus_1__485241

Identity

Accession:
YP_002308362 ↗
Protein ID:
L2_capsid_protein
Kingdom:
euk

Quality

53.2 mean pLDDT

Taxonomy

Shotokuvirae› Cossaviricota› Papovaviricetes› Zurhausenvirales› Papillomaviridae› Dyozetapapillomavirus› Caretta_caretta_papillomavirus_1

TaxID: 485241

Cluster

Singleton — not in a non-trivial cluster

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 225-255_277-326
PDB
Domain cluster: rep: L2_capsid_protein__YP_009272578__Bos_taurus_papillomavirus_13__1887213__D263-325
CATH (34)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4damC00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.69 42.0 3.96e-01 82.7% 50.0%
1olzA01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.67 47.0 2.94e-01 74.1% 16.8%
2be3B01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.61 53.0 4.51e-01 97.5% 58.5%
4qa8A00 2.50.20.20 Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › 0.60 44.0 3.23e-01 77.8% 75.7%
3fhwA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.59 37.0 3.46e-01 82.7% 50.5%
1fguB01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.59 36.0 3.33e-01 85.2% 46.7%
1fmbA00 2.40.70.10 Mainly Beta › Beta Barrel › Cathepsin D, subunit A; domain 1 › Acid Proteases 0.57 40.0 3.70e-01 93.8% 55.8%
3j7aV00 2.40.50.1000 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.56 32.0 2.70e-01 79.0% 29.5%
3t0qA00 3.40.850.10 Alpha Beta › 3-Layer(aba) Sandwich › Kinesin › Kinesin motor domain 0.55 43.0 2.97e-01 86.4% 44.7%
1iz6A01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.55 37.0 3.96e-01 79.0% 81.2%
2kinA00 3.40.850.10 Alpha Beta › 3-Layer(aba) Sandwich › Kinesin › Kinesin motor domain 0.55 43.0 3.12e-01 85.2% 64.7%
4lgqA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.55 40.0 3.45e-01 77.8% 78.9%
2jq5A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.55 41.0 3.52e-01 79.0% 65.6%
2rfrA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.55 40.0 3.29e-01 77.8% 67.5%
1z5bB03 3.30.230.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.54 40.0 3.28e-01 77.8% 69.1%
6rtqA00 2.40.128.30 Mainly Beta › Beta Barrel › Lipocalin › Avidin-like 0.54 42.0 3.65e-01 86.4% 82.7%
4awdB00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.54 37.0 2.57e-01 71.6% 46.9%
3qz4A00 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.54 47.0 3.24e-01 100.0% 90.2%
2vsmA00 2.120.10.10 Mainly Beta › 6 Propeller › Neuraminidase › 0.54 48.0 3.03e-01 100.0% 89.6%
1b9vA00 2.120.10.10 Mainly Beta › 6 Propeller › Neuraminidase › 0.53 45.0 3.01e-01 100.0% 84.1%
6dnzA02 2.70.160.11 Mainly Beta › Distorted Sandwich › Hnrnp arginine n-methyltransferase1 › Hnrnp arginine n-methyltransferase1 0.53 41.0 3.27e-01 86.4% 80.9%
4gb5A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 37.0 3.15e-01 75.3% 73.6%
2c4mA01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.53 42.0 2.69e-01 91.4% 38.8%
2zwsA02 2.60.40.2300 Mainly Beta › Sandwich › Immunoglobulin-like › Neutral/alkaline non-lysosomal ceramidase, C-terminal domain 0.52 40.0 3.45e-01 84.0% 85.8%
1s5aB00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.52 37.0 3.18e-01 77.8% 73.4%
5dstA02 2.70.160.11 Mainly Beta › Distorted Sandwich › Hnrnp arginine n-methyltransferase1 › Hnrnp arginine n-methyltransferase1 0.52 40.0 3.18e-01 85.2% 80.2%
3kf8A00 2.40.50.1040 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.52 36.0 2.69e-01 87.7% 28.5%
3t1oA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 44.0 3.33e-01 93.8% 40.1%
4gkpB00 3.40.850.20 Alpha Beta › 3-Layer(aba) Sandwich › Kinesin › 0.51 40.0 2.86e-01 85.2% 44.5%
5ig0A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.51 37.0 3.27e-01 79.0% 80.2%
3soyA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.51 37.0 3.16e-01 77.8% 76.1%
7tm7B01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.51 40.0 2.61e-01 91.4% 41.6%
3bb9B00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.50 37.0 3.26e-01 79.0% 77.6%
7clyA01 2.60.40.150 Mainly Beta › Sandwich › Immunoglobulin-like › C2 domain 0.50 35.0 2.83e-01 74.1% 60.8%
ECOD (61)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4947823 211.1.1.0 ↗ a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase 0.67 48.0 4.52e-01 87.7% 61.0%
5041944 2.1.1.15 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › tRNA_anti-codon 0.64 38.0 3.49e-01 86.4% 45.7%
4137219 2.1.1.6 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › SSB 0.64 39.0 3.63e-01 85.2% 49.0%
3185466 4.1.1.225 ↗ beta barrels › SH3 › SH3 › SH3 › DUF7025 0.64 47.0 3.49e-01 77.8% 32.5%
3600656 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.63 47.0 3.07e-01 80.2% 25.9%
4974918 2.1.1.15 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › tRNA_anti-codon 0.63 38.0 3.50e-01 87.7% 46.7%
4940586 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.63 38.0 3.32e-01 86.4% 40.8%
5030516 2.1.1.15 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › tRNA_anti-codon 0.62 38.0 3.49e-01 87.7% 46.7%
4973410 881.1.1.0 ↗ a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like 0.62 49.0 3.99e-01 87.7% 54.4%
3603247 2.1.1.15 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › tRNA_anti-codon 0.62 37.0 3.24e-01 85.2% 40.0%
5016563 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.62 41.0 3.62e-01 87.7% 46.7%
3188394 4.8.1.22 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like › DUF7025 0.62 46.0 4.00e-01 77.8% 57.5%
3625857 2.1.1.15 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › tRNA_anti-codon 0.61 38.0 3.24e-01 85.2% 38.5%
3631313 4.1.1.225 ↗ beta barrels › SH3 › SH3 › SH3 › DUF7025 0.61 45.0 3.40e-01 77.8% 35.3%
3441179 2.1.1.130 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DUF223 0.61 37.0 3.26e-01 85.2% 40.0%
5055280 331.4.1.0 ↗ a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 0.59 47.0 3.94e-01 87.7% 58.6%
5021941 2008.1.1.0 ↗ a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.59 44.0 3.36e-01 79.0% 38.3%
4646070 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.58 35.0 3.21e-01 85.2% 43.6%
3921111 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.58 45.0 4.11e-01 82.7% 93.3%
3717566 5.1.3.28 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › BNR_3 0.58 39.0 2.79e-01 91.4% 21.7%
5006022 4272.1.1.1 ↗ a+b two layers › Nqo5-like › Nqo5-like › Nqo5-like › Complex1_30kDa 0.58 45.0 3.62e-01 90.1% 42.3%
5031038 1.1.1.18 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease › Asp_protease_2 0.57 40.0 3.50e-01 93.8% 47.2%
3901529 11.1.1.640 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › ZP-N 0.57 45.0 4.27e-01 82.7% 93.7%
3922370 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.56 43.0 3.82e-01 82.7% 95.8%
5009330 4272.1.1.1 ↗ a+b two layers › Nqo5-like › Nqo5-like › Nqo5-like › Complex1_30kDa 0.56 44.0 3.50e-01 88.9% 42.5%
5055337 881.1.1.0 ↗ a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like 0.56 46.0 3.76e-01 92.6% 70.6%
3598574 2004.1.1.250 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Kinesin,Microtub_bd 0.56 43.0 2.81e-01 86.4% 45.6%
3663259 881.1.1.1 ↗ a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like › PsbP 0.55 44.0 3.78e-01 87.7% 63.7%
3228695 11.10.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › TRAF domain-like › TRAF domain-like 0.55 41.0 3.34e-01 100.0% 41.9%
3435224 243.3.1.19 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › DUF3615 0.55 39.0 4.31e-01 76.5% 93.8%
3462235 243.3.1.19 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › DUF3615 0.55 41.0 4.13e-01 79.0% 81.2%
3947973 243.1.1.18 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › SnoaL_2 0.54 40.0 3.53e-01 79.0% 79.2%
3829111 881.1.1.1 ↗ a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like › PsbP 0.54 47.0 3.56e-01 100.0% 76.7%
3881009 11.1.1.640 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › ZP-N 0.54 41.0 3.72e-01 82.7% 87.0%
3897520 11.1.1.640 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › ZP-N 0.54 42.0 3.98e-01 82.7% 96.8%
5046983 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.54 46.0 2.99e-01 98.8% 90.1%
2672137 5.1.3.3 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Neur 0.54 46.0 3.03e-01 100.0% 83.9%
5034595 4272.1.1.1 ↗ a+b two layers › Nqo5-like › Nqo5-like › Nqo5-like › Complex1_30kDa 0.54 43.0 3.41e-01 88.9% 44.3%
5079769 2004.1.1.14 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › GTP_EFTU 0.53 44.0 3.34e-01 91.4% 38.0%
4640369 319.1.1.1 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › HSP20 0.53 31.0 2.94e-01 77.8% 43.8%
4059480 881.1.1.37 ↗ a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like › PF27270 0.53 44.0 3.46e-01 92.6% 57.1%
4974879 881.1.1.0 ↗ a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like 0.53 43.0 3.47e-01 91.4% 52.7%
4929156 4272.1.1.1 ↗ a+b two layers › Nqo5-like › Nqo5-like › Nqo5-like › Complex1_30kDa 0.53 41.0 3.32e-01 88.9% 42.9%
3844481 11.1.1.640 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › ZP-N 0.52 40.0 3.65e-01 82.7% 85.5%
4990210 283.2.1.8 ↗ a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like › PF29994 0.52 40.0 3.81e-01 82.7% 89.5%
4024062 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.52 30.0 3.10e-01 79.0% 56.8%
3301049 4272.1.1.1 ↗ a+b two layers › Nqo5-like › Nqo5-like › Nqo5-like › Complex1_30kDa 0.52 40.0 3.58e-01 85.2% 61.7%
3839556 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.52 38.0 2.67e-01 79.0% 48.0%
5014316 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.51 45.0 3.66e-01 100.0% 88.7%
3789933 11.10.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › TRAF domain-like › TRAF domain-like 0.51 37.0 3.39e-01 100.0% 58.1%
3562855 11.1.1.614 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_ZP2 0.51 39.0 3.58e-01 85.2% 98.3%
3966871 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.51 44.0 3.81e-01 97.5% 64.6%
3613921 330.1.1.22 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › PF26536 0.51 38.0 3.34e-01 85.2% 52.0%
2409688 2004.1.1.16 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Arf 0.51 43.0 3.25e-01 93.8% 38.1%
4353676 223.1.1.41 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › HisK_sensor 0.51 39.0 3.39e-01 85.2% 77.8%
3258455 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.51 36.0 3.32e-01 80.2% 56.0%
3217893 11.1.1.97 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › I-set 0.51 40.0 3.27e-01 88.9% 57.0%
4643563 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.51 37.0 3.65e-01 79.0% 74.4%
3301984 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.51 33.0 3.74e-01 70.4% 98.2%
4934627 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.50 41.0 3.73e-01 100.0% 64.3%
5019574 223.1.1.2 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS 0.50 38.0 3.49e-01 85.2% 98.3%