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VP1

Euk-Vir

Raccoon-associated_polyomavirus_2

VP1__YP_009357241__Raccoon-associated_polyomavirus_2__1978920

Identity

Accession:
YP_009357241 ↗
Protein ID:
VP1
Kingdom:
euk

Quality

69.3 mean pLDDT

Taxonomy

Shotokuvirae› Cossaviricota› Papovaviricetes› Sepolyvirales› Polyomaviridae› Deltapolyomavirus› Raccoon-associated_polyomavirus_2

TaxID: 1978920

Cluster

View cluster (117 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 medium residues 40-65_84-127_235-250_279-296
PDB
Domain cluster: rep: VP1__YP_009551976__Tupaia_glis_polyomavirus_1__2170402__D33-54_101-134_245-326
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00718.29 best Polyoma_coat 77.6 1.20e-21 44.2% 14.9%
D2 medium residues 128-155_215-234_251-278
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00718.29 best Polyoma_coat 46.2 4.50e-12 64.5% 21.6%
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3s7vC00 2.60.175.10 Mainly Beta › Sandwich › Polyomavirus Vp1; Chain A › Capsid protein VP1,Polyomavirus 0.82 77.0 5.10e-01 100.0% 53.7%
5hbaA00 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.55 41.0 3.44e-01 80.3% 47.4%
1djxA03 2.60.40.150 Mainly Beta › Sandwich › Immunoglobulin-like › C2 domain 0.52 38.0 3.22e-01 78.9% 50.4%
2xskA00 2.60.40.2420 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 45.0 4.25e-01 100.0% 92.6%
7q61A01 2.60.40.1940 Mainly Beta › Sandwich › Immunoglobulin-like › 0.50 42.0 3.77e-01 100.0% 66.1%
2n59A00 2.60.40.2420 Mainly Beta › Sandwich › Immunoglobulin-like › 0.50 40.0 3.72e-01 100.0% 67.3%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5047571 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.55 44.0 3.97e-01 100.0% 61.8%
4011054 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.54 41.0 3.51e-01 81.6% 62.4%
3409524 11.1.1.9 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Arrestin_N 0.54 41.0 3.34e-01 85.5% 54.8%
5041022 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.52 41.0 3.54e-01 100.0% 52.3%
3998442 11.2.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › C2 domain › C2 domain 0.51 43.0 3.47e-01 100.0% 54.1%
D3 medium residues 156-214_314-336
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00718.29 best Polyoma_coat 71.6 8.40e-20 85.4% 20.3%
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1sidF00 2.60.175.10 Mainly Beta › Sandwich › Polyomavirus Vp1; Chain A › Capsid protein VP1,Polyomavirus 0.72 66.0 4.17e-01 96.3% 40.1%
3s7vC00 2.60.175.10 Mainly Beta › Sandwich › Polyomavirus Vp1; Chain A › Capsid protein VP1,Polyomavirus 0.68 61.0 4.17e-01 96.3% 49.3%
6uzjA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.56 38.0 4.21e-01 70.7% 96.8%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
961478 10.2.1.6 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Polyoma_coat 0.90 67.0 4.54e-01 76.8% 43.5%
2666438 10.2.1.6 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Polyoma_coat 0.72 66.0 4.24e-01 96.3% 41.8%
423236 10.2.1.6 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Polyoma_coat 0.68 61.0 4.18e-01 96.3% 49.6%
3207948 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.52 35.0 2.78e-01 72.0% 69.0%