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VP1

Euk-Vir

Betapolyomavirus_securanorvegicus

VP1__YP_009325930__Betapolyomavirus_securanorvegicus__1919247

Identity

Accession:
YP_009325930 ↗
Protein ID:
VP1
Kingdom:
euk

Quality

76.3 mean pLDDT

Taxonomy

Shotokuvirae› Cossaviricota› Papovaviricetes› Sepolyvirales› Polyomaviridae› Betapolyomavirus› Betapolyomavirus_securanorvegicus

TaxID: 1919247

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 high residues 30-309
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00718.29 best Polyoma_coat 205.8 1.10e-60 97.9% 97.3%
CATH (41)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3s7vC00 2.60.175.10 Mainly Beta › Sandwich › Polyomavirus Vp1; Chain A › Capsid protein VP1,Polyomavirus 0.97 86.0 8.86e-01 90.4% 100.0%
1sidF00 2.60.175.10 Mainly Beta › Sandwich › Polyomavirus Vp1; Chain A › Capsid protein VP1,Polyomavirus 0.88 79.0 7.17e-01 92.1% 81.9%
2id4A02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.70 35.0 4.94e-01 88.2% 97.1%
1o6uA02 2.60.120.680 Mainly Beta › Sandwich › Jelly Rolls › GOLD domain 0.68 28.0 4.46e-01 82.9% 98.1%
2df7A02 2.60.120.660 Mainly Beta › Sandwich › Jelly Rolls › icosahedral virus 0.67 35.0 4.84e-01 85.4% 99.3%
1f15B00 2.60.120.530 Mainly Beta › Sandwich › Jelly Rolls › Cucumovirus coat protein, subunit A 0.66 36.0 4.30e-01 87.5% 76.3%
3cu7A10 2.60.120.1540 Mainly Beta › Sandwich › Jelly Rolls › 0.66 28.0 4.31e-01 86.4% 95.7%
1dzlA00 2.60.175.20 Mainly Beta › Sandwich › Polyomavirus Vp1; Chain A › Major capsid L1 (late) superfamily, Papillomavirus 0.65 61.0 5.14e-01 100.0% 95.4%
1e57B00 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.61 37.0 4.45e-01 89.3% 89.6%
4zchA01 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.61 30.0 4.30e-01 82.5% 100.0%
4nwvA01 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.61 37.0 4.45e-01 86.1% 89.7%
6f2sH01 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.60 41.0 4.62e-01 87.9% 87.9%
1auyB00 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.60 37.0 4.35e-01 89.3% 86.8%
4aw7A01 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.59 22.0 3.26e-01 77.1% 73.7%
6ovbA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.59 31.0 4.06e-01 85.0% 89.6%
3c7fA01 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.59 30.0 4.11e-01 83.6% 95.1%
5c8cB00 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.58 43.0 4.31e-01 95.4% 72.7%
3wnoA03 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.58 28.0 4.06e-01 82.5% 98.5%
2okxA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.58 31.0 3.88e-01 82.9% 82.9%
2wzpP03 2.60.120.880 Mainly Beta › Sandwich › Jelly Rolls › 0.58 28.0 4.08e-01 84.3% 100.0%
4w8jA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.58 30.0 3.94e-01 84.6% 88.5%
4ofqA02 2.60.40.740 Mainly Beta › Sandwich › Immunoglobulin-like › 0.57 32.0 4.14e-01 92.5% 95.5%
1o91A00 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.57 28.0 4.04e-01 85.0% 100.0%
1gwmA00 2.60.120.430 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding lectin 0.57 29.0 3.86e-01 87.1% 88.9%
1f2nC00 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.56 36.0 4.10e-01 86.4% 84.0%
3nqhA02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.55 28.0 3.85e-01 82.1% 96.3%
3j26N01 2.60.120.1100 Mainly Beta › Sandwich › Jelly Rolls › 0.55 34.0 4.26e-01 86.4% 99.4%
7pzaA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.55 21.0 3.17e-01 88.6% 78.7%
2re9A01 2.60.120.40 Mainly Beta › Sandwich › Jelly Rolls › 0.54 31.0 4.07e-01 83.9% 100.0%
1tme200 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.53 41.0 4.30e-01 96.4% 86.7%
1smvC00 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.52 37.0 4.12e-01 93.6% 89.6%
1pgsA02 2.60.120.230 Mainly Beta › Sandwich › Jelly Rolls › 0.52 33.0 4.06e-01 95.7% 100.0%
4uzgA01 2.60.40.740 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 30.0 3.82e-01 92.5% 97.4%
4jdzA02 2.60.40.1290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 29.0 3.68e-01 93.6% 92.1%
4ym3C00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.51 27.0 3.70e-01 81.1% 100.0%
3no8A00 2.60.120.820 Mainly Beta › Sandwich › Jelly Rolls › PHR domain 0.51 29.0 3.74e-01 97.1% 96.8%
5gm0A01 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.51 27.0 3.63e-01 75.7% 95.9%
1w2tA02 2.60.120.560 Mainly Beta › Sandwich › Jelly Rolls › Exo-inulinase; domain 1 0.51 25.0 3.47e-01 82.9% 94.0%
2bv4A00 2.60.120.400 Mainly Beta › Sandwich › Jelly Rolls › Calcium-mediated lectin 0.51 22.0 3.39e-01 76.1% 99.1%
5jzgA00 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.51 33.0 3.66e-01 93.9% 80.5%
1w99A02 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.50 33.0 3.90e-01 86.4% 94.2%
ECOD (55)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
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 0.95 84.0 8.68e-01 90.4% 99.6%
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 0.89 81.0 7.44e-01 92.9% 85.9%
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 0.87 72.0 7.60e-01 83.9% 100.0%
5040234 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.72 31.0 4.80e-01 86.4% 98.3%
3381013 10.32.1.72 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › TPPII_GBD 0.70 31.0 4.01e-01 82.1% 70.6%
3256150 10.4.1.0 ↗ beta sandwiches › jelly-roll › Spermadhesin, CUB domain › Spermadhesin, CUB domain 0.69 29.0 4.40e-01 83.6% 93.0%
3791166 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.68 30.0 4.36e-01 83.2% 90.3%
5026113 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.68 27.0 4.39e-01 83.6% 100.0%
5084067 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.67 26.0 4.31e-01 81.8% 100.0%
3849644 10.32.1.6 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › P_proprotein 0.67 34.0 4.81e-01 86.8% 100.0%
5063656 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.67 30.0 4.51e-01 83.9% 99.1%
4002865 10.32.1.6 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › P_proprotein 0.67 35.0 4.83e-01 87.1% 100.0%
3714436 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.65 31.0 4.53e-01 94.6% 97.7%
3597814 10.32.1.3 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Calpain_III 0.65 34.0 4.56e-01 93.2% 92.7%
2707156 10.2.1.4 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Late_protein_L1 0.65 62.0 5.04e-01 100.0% 89.9%
3703651 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.65 30.0 4.40e-01 95.0% 96.8%
3772975 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.65 28.0 4.30e-01 93.2% 100.0%
3845477 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.64 29.0 4.14e-01 82.9% 88.5%
3708922 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.63 31.0 4.45e-01 93.2% 99.2%
3514837 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.63 27.0 4.06e-01 82.9% 93.9%
3607284 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.62 31.0 4.38e-01 93.6% 99.2%
3720149 10.2.1.0 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) 0.62 29.0 4.30e-01 83.9% 100.0%
5067925 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.62 27.0 4.11e-01 75.0% 99.1%
4452124 10.32.1.8 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › CBM_4_9 0.61 34.0 4.39e-01 86.8% 92.5%
3892939 10.32.1.229 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › PF27640 0.61 32.0 4.37e-01 83.2% 98.6%
1693522 10.2.1.49 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Capsid-VNN 0.61 37.0 4.44e-01 86.1% 89.2%
3692007 10.32.1.3 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Calpain_III 0.60 33.0 4.38e-01 93.6% 98.6%
3181785 10.32.1.23 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Bac_rhamnosid 0.60 30.0 4.24e-01 87.1% 99.2%
5041324 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.59 37.0 4.61e-01 82.5% 100.0%
5021065 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.58 32.0 4.11e-01 95.0% 90.3%
2141919 11.1.5.1 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f › Fimbrial 0.58 31.0 4.27e-01 83.6% 100.0%
3719095 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.58 33.0 4.16e-01 92.9% 93.8%
3780635 10.32.1.184 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Androglobin_II 0.58 31.0 4.23e-01 90.4% 99.3%
5052641 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.58 44.0 4.95e-01 87.1% 100.0%
4864830 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.57 29.0 4.13e-01 83.6% 100.0%
5054924 4182.1.1.0 ↗ beta sandwiches › Agglutinin HPA-like › Agglutinin HPA-like › Agglutinin HPA-like 0.57 30.0 4.01e-01 94.3% 93.3%
4547180 10.32.1.18 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Endotoxin_C 0.57 31.0 4.10e-01 85.0% 96.0%
3186189 10.2.1.0 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) 0.57 33.0 4.22e-01 86.1% 95.8%
3472901 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.57 29.0 4.04e-01 82.1% 100.0%
3415432 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.57 29.0 4.07e-01 81.1% 100.0%
4054625 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.55 32.0 4.03e-01 83.2% 92.9%
3407663 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.55 29.0 4.02e-01 85.4% 100.0%
5083932 10.1.2.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) 0.55 30.0 3.98e-01 80.7% 100.0%
3415694 10.40.1.0 ↗ beta sandwiches › jelly-roll › PHR domain › PHR domain 0.54 31.0 3.94e-01 95.0% 96.1%
3992792 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.54 31.0 4.06e-01 82.9% 99.4%
3482386 10.32.1.5 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Ephrin_lbd 0.54 33.0 4.16e-01 83.9% 99.4%
3626905 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.54 34.0 4.21e-01 97.1% 100.0%
3400017 10.40.1.0 ↗ beta sandwiches › jelly-roll › PHR domain › PHR domain 0.54 32.0 4.07e-01 83.2% 100.0%
3844538 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.53 29.0 3.77e-01 83.6% 91.9%
5035675 4182.1.1.0 ↗ beta sandwiches › Agglutinin HPA-like › Agglutinin HPA-like › Agglutinin HPA-like 0.53 32.0 3.98e-01 97.9% 96.5%
3313648 11.1.1.161 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › TPPII 0.52 24.0 3.60e-01 81.1% 100.0%
1232 10.2.1.7 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Viral_coat 0.52 36.0 4.23e-01 93.9% 100.0%
1076327 10.1.1.4 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Gal-bind_lectin 0.51 28.0 3.67e-01 79.3% 96.7%
3597772 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.50 32.0 3.78e-01 92.9% 90.3%
3489233 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.50 39.0 4.28e-01 83.6% 97.8%