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capsid_protein

Euk-Vir

Red_clover_powdery_mildew-associated_totivirus_3

capsid_protein__YP_009182180__Red_clover_powdery_mildew-associated_totivirus_3__1714364

Identity

Accession:
YP_009182180 ↗
Protein ID:
capsid_protein
Kingdom:
euk

Quality

72.6 mean pLDDT

Taxonomy

Orthornavirae› Duplornaviricota› Chrymotiviricetes› Ghabrivirales› Orthototiviridae› Totivirus› Red_clover_powdery_mildew-associated_totivirus_3

TaxID: 1714364

Cluster

View cluster (13 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 1-45_360-460
PDB
Domain cluster: representative
D2 high residues 491-587
PDB
Domain cluster: representative
CATH (16)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1m1cA00 3.90.1840.10 Alpha Beta › Alpha-Beta Complex › Major capsid protein › Major capsid protein 0.71 64.0 3.85e-01 100.0% 15.5%
4ca1B02 2.60.210.10 Mainly Beta › Sandwich › Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A › Apoptosis, Tumor Necrosis Factor Receptor Associated Protein 2; Chain A 0.61 44.0 4.01e-01 75.3% 95.5%
1xffA00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.58 49.0 3.77e-01 95.9% 80.7%
3gidB02 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.57 39.0 4.19e-01 72.2% 83.1%
1ktbA02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.56 40.0 4.17e-01 75.3% 97.8%
3bpnC03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 45.0 4.48e-01 90.7% 94.1%
2aehA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.54 39.0 3.94e-01 75.3% 95.8%
4ecnA02 2.60.40.3540 Mainly Beta › Sandwich › Immunoglobulin-like › Domain of unknown function DUF4458 0.54 43.0 3.99e-01 85.6% 92.6%
3cvzB01 3.30.1490.290 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › Low molecular weight S-layer protein, domain 1 0.54 42.0 4.27e-01 88.7% 97.0%
2zuoA09 2.30.30.570 Mainly Beta › Roll › SH3 type barrels. › 0.54 33.0 3.92e-01 75.3% 93.7%
3gydA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.53 37.0 3.10e-01 74.2% 70.2%
1aw8B00 2.40.40.20 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › 0.53 41.0 4.22e-01 83.5% 98.9%
3qt2B03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 42.0 4.28e-01 91.8% 87.8%
2ww8A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 42.0 4.10e-01 88.7% 94.3%
2hq7B00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.52 38.0 3.38e-01 76.3% 91.5%
2ed8A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 39.0 4.11e-01 91.8% 95.3%
ECOD (19)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
7654 4065.1.1.1 ↗ a+b complex topology › L-A virus major coat protein-related › L-A virus major coat protein-related › L-A virus major coat protein-related › LA-virus_coat 0.71 64.0 3.85e-01 100.0% 15.5%
4930010 1.1.7.141 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › MazE_antitoxin 0.62 43.0 4.43e-01 72.2% 85.3%
3311693 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.61 42.0 4.12e-01 71.1% 98.1%
3963821 210.1.3.5 ↗ a+b four layers › Ntn/PP2C › Ntn › Class II glutamine amidotransferases › GATase_7 0.58 51.0 3.83e-01 97.9% 97.6%
4994995 210.1.3.5 ↗ a+b four layers › Ntn/PP2C › Ntn › Class II glutamine amidotransferases › GATase_7 0.58 50.0 3.86e-01 97.9% 83.8%
4321843 210.1.3.5 ↗ a+b four layers › Ntn/PP2C › Ntn › Class II glutamine amidotransferases › GATase_7 0.58 49.0 3.86e-01 97.9% 88.0%
4259223 210.1.3.5 ↗ a+b four layers › Ntn/PP2C › Ntn › Class II glutamine amidotransferases › GATase_7 0.57 49.0 3.78e-01 96.9% 82.6%
3608700 320.4.1.0 ↗ a+b two layers › R3H domain-like › PUB domain › PUB domain 0.57 50.0 4.09e-01 99.0% 72.6%
None — 0.57 49.0 3.77e-01 97.9% 83.7%
3914036 221.1.1.87 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › FERM_N_2 0.57 41.0 4.00e-01 75.3% 90.5%
4928834 210.1.3.0 ↗ a+b four layers › Ntn/PP2C › Ntn › Class II glutamine amidotransferases 0.56 48.0 3.79e-01 99.0% 84.5%
2323861 1137.1.1.0 ↗ a+b two layers › Tetrapyrrole methylase C-terminal domain-like › Tetrapyrrole methylase C-terminal domain › Tetrapyrrole methylase C-terminal domain 0.53 44.0 3.67e-01 88.7% 58.2%
3487680 4261.1.1.0 ↗ a+b two layers › TrkA C-terminal domain-like › TrkA C-terminal domain-like › TrkA C-terminal domain-like 0.53 41.0 3.83e-01 97.9% 65.6%
3494105 221.1.1.64 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › Formin_GBD_N 0.53 38.0 4.07e-01 74.2% 96.2%
5011866 210.1.3.3 ↗ a+b four layers › Ntn/PP2C › Ntn › Class II glutamine amidotransferases › GATase_4 0.53 45.0 3.54e-01 99.0% 93.2%
3229943 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.52 42.0 3.57e-01 88.7% 96.9%
3935404 221.1.1.76 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.51 36.0 3.80e-01 74.2% 98.9%
5013999 10.2.1.0 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) 0.51 43.0 3.71e-01 95.9% 86.1%
3969809 217.1.1.2 ↗ a+b complex topology › FAD-binding domain-like › FAD-binding domain › FAD-binding domain › FAD_binding_4 0.51 37.0 3.10e-01 78.4% 68.3%
D3 medium residues 61-135_270-353
PDB
Domain cluster: representative
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF09220.17 best LA-virus_coat 62.6 3.20e-17 52.2% 17.8%
PF09220.17 LA-virus_coat 39.0 4.70e-10 48.4% 15.8%
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1m1cA00 3.90.1840.10 Alpha Beta › Alpha-Beta Complex › Major capsid protein › Major capsid protein 0.90 86.0 5.48e-01 100.0% 45.6%
3jsbA01 1.20.1440.300 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › RNA-directed RNA polymerase L, helical domain 0.58 23.0 3.16e-01 94.3% 69.1%
7ewsA01 1.10.135.10 Mainly Alpha › Orthogonal Bundle › Transferase Creatine Kinase; Chain A, domain 1 › ATP:guanido phosphotransferase, N-terminal domain 0.58 27.0 3.30e-01 81.1% 67.3%
3edvB01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.51 26.0 2.87e-01 79.2% 57.4%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
7654 4065.1.1.1 ↗ a+b complex topology › L-A virus major coat protein-related › L-A virus major coat protein-related › L-A virus major coat protein-related › LA-virus_coat 0.90 86.0 5.48e-01 100.0% 45.6%
4821589 4065.1.1.1 ↗ a+b complex topology › L-A virus major coat protein-related › L-A virus major coat protein-related › L-A virus major coat protein-related › LA-virus_coat 0.87 82.0 5.93e-01 100.0% 69.6%
3743594 4065.1.1.1 ↗ a+b complex topology › L-A virus major coat protein-related › L-A virus major coat protein-related › L-A virus major coat protein-related › LA-virus_coat 0.86 82.0 5.96e-01 99.4% 55.1%