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capsid_protein_VP1
Euk-VirBat_bocavirus_XM30
capsid_protein_VP1__YP_009508795__Bat_bocavirus_XM30__2259811
Identity
- Accession:
- YP_009508795 ↗
- Protein ID:
- capsid_protein_VP1
- Kingdom:
- euk
Quality
75.3
mean pLDDT
Taxonomy
Shotokuvirae›
Cossaviricota›
Quintoviricetes›
Piccovirales›
Parvoviridae›
Bocaparvovirus›
Bat_bocavirus_XM30
TaxID: 2259811
Cluster
View cluster (92 members)3D Structure
Domains
high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.
D1
medium
residues 8-95
Domain cluster:
representative
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF08398.16 best | Phospholip_A2_4 | 106.5 | 9.20e-31 | 90.9% | 98.8% |
CATH (26)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 5wzoA00 | 1.20.90.10 | Mainly Alpha › Up-down Bundle › Phospholipase A2 › Phospholipase A2 domain | 0.79 | 59.0 | 5.16e-01 | 77.3% | 72.4% |
| 1wbeA01 | 1.10.3520.10 | Mainly Alpha › Orthogonal Bundle › Glycolipid transfer protein, GLTP › Glycolipid transfer protein | 0.60 | 46.0 | 3.66e-01 | 83.0% | 97.3% |
| 1yuzB01 | 1.20.1260.10 | Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle | 0.58 | 48.0 | 4.21e-01 | 92.0% | 95.7% |
| 3rjvA01 | 1.25.40.10 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain | 0.57 | 47.0 | 4.11e-01 | 94.3% | 80.6% |
| 2om6A02 | 1.10.150.400 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › | 0.57 | 43.0 | 4.51e-01 | 86.4% | 88.6% |
| 3u61D03 | 1.20.272.10 | Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › | 0.56 | 36.0 | 3.62e-01 | 77.3% | 62.6% |
| 1rq5A02 | 1.50.10.10 | Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › | 0.56 | 50.0 | 3.11e-01 | 100.0% | 61.1% |
| 5figA00 | 1.20.1270.360 | Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › | 0.56 | 49.0 | 4.72e-01 | 97.7% | 87.0% |
| 6pw7A02 | 1.10.150.50 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Transcription Factor, Ets-1 | 0.55 | 37.0 | 4.11e-01 | 95.5% | 87.3% |
| 2x3fA02 | 3.30.1300.10 | Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › Pantoate-beta-alanine ligase, C-terminal domain | 0.55 | 42.0 | 4.05e-01 | 94.3% | 72.0% |
| 1fftC00 | 1.20.120.80 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c oxidase, subunit III, four-helix bundle | 0.54 | 46.0 | 3.67e-01 | 96.6% | 74.6% |
| 3ns4A00 | 1.10.357.110 | Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Vacuolar protein sorting-associated protein 53, C-terminus | 0.54 | 44.0 | 3.42e-01 | 92.0% | 64.4% |
| 2no4A02 | 1.10.150.240 | Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 | 0.53 | 40.0 | 4.31e-01 | 88.6% | 96.0% |
| 2c2jA00 | 1.20.1260.10 | Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle | 0.53 | 46.0 | 3.78e-01 | 97.7% | 69.1% |
| 4d3pA00 | 3.90.190.10 | Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily | 0.52 | 45.0 | 3.87e-01 | 98.9% | 97.3% |
| 5hayA02 | 1.25.40.440 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Nucleoporin, helical domain, central subdomain | 0.52 | 42.0 | 4.45e-01 | 98.9% | 100.0% |
| 3ma5A00 | 1.25.40.10 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain | 0.52 | 41.0 | 4.13e-01 | 88.6% | 94.4% |
| 1tvzA02 | 3.40.47.10 | Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase | 0.52 | 40.0 | 3.48e-01 | 86.4% | 78.2% |
| 1w6jA02 | 1.50.10.20 | Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › | 0.52 | 44.0 | 2.95e-01 | 95.5% | 49.2% |
| 7wf8B01 | 1.10.167.10 | Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › Regulator of G-protein Signalling 4, domain 2 | 0.51 | 42.0 | 3.84e-01 | 98.9% | 66.9% |
| 2vxdA00 | 1.10.10.2100 | Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Nucleophosmin, C-terminal domain | 0.51 | 32.0 | 3.71e-01 | 87.5% | 100.0% |
| 2j16A00 | 3.90.190.10 | Alpha Beta › Alpha-Beta Complex › Protein-Tyrosine Phosphatase; Chain A › Protein tyrosine phosphatase superfamily | 0.51 | 44.0 | 3.91e-01 | 98.9% | 97.7% |
| 3h78A02 | 3.40.47.10 | Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase | 0.51 | 39.0 | 3.37e-01 | 86.4% | 65.2% |
| 1eblA02 | 3.40.47.10 | Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase | 0.51 | 39.0 | 3.39e-01 | 85.2% | 70.1% |
| 2i6hA02 | 1.25.40.10 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain | 0.50 | 38.0 | 3.76e-01 | 97.7% | 75.0% |
| 4l9pA00 | 1.25.40.120 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Protein prenylyltransferase | 0.50 | 43.0 | 3.00e-01 | 100.0% | 35.2% |
ECOD (18)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3725618 | 601.26.1.0 ↗ | alpha bundles › Four-helical up-and-down bundle › YppE-like › YppE-like | 0.62 | 43.0 | 3.80e-01 | 73.9% | 71.1% |
| 5060704 | 371.1.1.5 ↗ | few secondary structure elements › Phospholipase A2, PLA2 › Phospholipase A2, PLA2 › Phospholipase A2, PLA2 › DUF1353 | 0.62 | 47.0 | 4.36e-01 | 86.4% | 64.5% |
| 3238221 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.60 | 48.0 | 3.35e-01 | 97.7% | 25.2% |
| 1878754 | 604.1.1.0 ↗ | alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat | 0.60 | 41.0 | 4.19e-01 | 70.5% | 95.2% |
| 3655933 | 604.12.1.2 ↗ | alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › Vta1 | 0.60 | 53.0 | 5.12e-01 | 97.7% | 89.0% |
| 4167208 | 604.15.1.0 ↗ | alpha bundles › Spectrin repeat-like › Efb C-domain-like › Efb C-domain-like | 0.59 | 38.0 | 4.36e-01 | 88.6% | 95.0% |
| 3178397 | 109.4.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat | 0.57 | 42.0 | 3.29e-01 | 77.3% | 66.8% |
| 5053234 | 101.1.4.0 ↗ | alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like | 0.57 | 45.0 | 4.54e-01 | 96.6% | 86.7% |
| 4997481 | 633.21.1.0 ↗ | alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 | 0.56 | 48.0 | 4.62e-01 | 94.3% | 89.0% |
| 4676398 | 2004.1.1.94 ↗ | a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ATP_bind_1 | 0.55 | 44.0 | 3.32e-01 | 90.9% | 44.5% |
| 3438993 | 109.4.1.912 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › ARM_KDM8_N | 0.55 | 46.0 | 4.16e-01 | 96.6% | 91.5% |
| 3621256 | 633.23.1.4 ↗ | alpha bundles › Bromodomain-like › Claudin › Claudin › Claudin_2 | 0.55 | 47.0 | 3.52e-01 | 97.7% | 81.2% |
| 3719700 | 109.2.1.80 ↗ | alpha superhelices › Repetitive alpha hairpins › alpha/alpha toroid › alpha/alpha toroid › PF30299 | 0.54 | 42.0 | 2.92e-01 | 85.2% | 64.1% |
| 3643402 | 592.1.1.0 ↗ | alpha arrays › PWI domain-like › PWI domain › PWI domain | 0.52 | 41.0 | 3.58e-01 | 87.5% | 62.9% |
| 3958030 | 7510.1.1.0 ↗ | a/b three-layered sandwiches › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like › Isocitrate/Isopropylmalate dehydrogenase-like | 0.51 | 43.0 | 2.87e-01 | 96.6% | 77.7% |
| 4060119 | 2003.1.4.3 ↗ | a/b three-layered sandwiches › Rossmann-like › Rossmann-related › DHS-like NAD/FAD-binding domain › DS | 0.51 | 41.0 | 2.81e-01 | 90.9% | 31.1% |
| 3599166 | 2003.1.4.0 ↗ | a/b three-layered sandwiches › Rossmann-like › Rossmann-related › DHS-like NAD/FAD-binding domain | 0.50 | 42.0 | 2.86e-01 | 93.2% | 31.3% |
| 3277409 | 109.3.1.0 ↗ | alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat | 0.50 | 40.0 | 3.13e-01 | 90.9% | 39.5% |
D2
medium
residues 188-240_310-390
Domain cluster:
rep: capsid_protein_2__YP_009272916__Mink_bocavirus_1__2259808__D75-100_121-246
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00740.24 best | VP1_2 | 29.3 | 4.80e-07 | 61.2% | 13.1% |
D3
medium
residues 241-309_580-653
Domain cluster:
rep: capsid__YP_004013958__Porcine_parvovirus_4__707546__D235-310_345-380_625-643_658-681
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00740.24 best | VP1_2 | 51.3 | 1.10e-13 | 51.0% | 13.1% |
CATH (10)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4qc8A00 | 2.170.30.10 | Mainly Beta › Beta Complex › Empty Capsid Viral Protein 2 › Parvovirus coat protein VP1/VP2 | 0.97 | 95.0 | 6.19e-01 | 100.0% | 77.9% |
| 2g8gA00 | 2.170.30.10 | Mainly Beta › Beta Complex › Empty Capsid Viral Protein 2 › Parvovirus coat protein VP1/VP2 | 0.96 | 93.0 | 6.01e-01 | 100.0% | 79.4% |
| 1s58A00 | 2.170.30.10 | Mainly Beta › Beta Complex › Empty Capsid Viral Protein 2 › Parvovirus coat protein VP1/VP2 | 0.93 | 90.0 | 5.82e-01 | 100.0% | 75.5% |
| 1c8dA00 | 2.170.30.10 | Mainly Beta › Beta Complex › Empty Capsid Viral Protein 2 › Parvovirus coat protein VP1/VP2 | 0.92 | 89.0 | 5.71e-01 | 100.0% | 78.3% |
| 1vwxP00 | 3.90.470.10 | Alpha Beta › Alpha-Beta Complex › Ribosomal Protein L22; Chain A › Ribosomal protein L22/L17 | 0.57 | 29.0 | 2.92e-01 | 97.2% | 43.8% |
| 5d6hA01 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.57 | 31.0 | 3.29e-01 | 93.7% | 57.1% |
| 4n0rA01 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.54 | 26.0 | 3.12e-01 | 93.7% | 68.2% |
| 1rtzA00 | 3.30.70.560 | Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 7,8-Dihydro-6-hydroxymethylpterin-pyrophosphokinase HPPK | 0.54 | 23.0 | 2.34e-01 | 100.0% | 34.2% |
| 3nziA01 | 2.40.10.10 | Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases | 0.53 | 25.0 | 2.83e-01 | 72.7% | 53.8% |
| 2pn5A08 | 2.60.120.1540 | Mainly Beta › Sandwich › Jelly Rolls › | 0.51 | 31.0 | 3.44e-01 | 100.0% | 76.6% |
ECOD (13)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 3107798 | 10.2.1.9 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Parvo_coat | 0.99 | 97.0 | 6.19e-01 | 100.0% | 79.6% |
| 2707659 | 10.2.1.9 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Parvo_coat | 0.99 | 97.0 | 6.22e-01 | 100.0% | 75.1% |
| 2644354 | 10.2.1.9 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Parvo_coat | 0.96 | 93.0 | 6.01e-01 | 100.0% | 79.3% |
| 2990572 | 10.2.1.9 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Parvo_coat | 0.95 | 93.0 | 5.96e-01 | 100.0% | 79.6% |
| 1195 | 10.2.1.9 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Parvo_coat | 0.93 | 90.0 | 5.82e-01 | 100.0% | 75.5% |
| 2142463 | 10.2.1.9 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Parvo_coat | 0.92 | 89.0 | 5.72e-01 | 100.0% | 76.5% |
| 4884619 | 10.2.1.9 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Parvo_coat | 0.92 | 89.0 | 5.68e-01 | 100.0% | 76.6% |
| 3473996 | 10.2.1.0 ↗ | beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) | 0.76 | 71.0 | 5.60e-01 | 100.0% | 82.5% |
| 3583548 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.61 | 31.0 | 3.98e-01 | 74.1% | 85.0% |
| 1125237 | 218.2.1.1 ↗ | a+b two layers › Enolase-N/ribosomal protein › Ribosomal protein L22 › Ribosomal protein L22 › Ribosomal_L22 | 0.61 | 31.0 | 3.51e-01 | 97.9% | 62.7% |
| 4286671 | 218.2.1.1 ↗ | a+b two layers › Enolase-N/ribosomal protein › Ribosomal protein L22 › Ribosomal protein L22 › Ribosomal_L22 | 0.59 | 31.0 | 2.92e-01 | 100.0% | 39.3% |
| 3411669 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.51 | 28.0 | 3.15e-01 | 97.2% | 68.2% |
| 3015706 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.50 | 30.0 | 3.19e-01 | 93.7% | 66.1% |
D4
medium
residues 439-579