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VP1

Euk-Vir

Norovirus_GII.17

VP1__YP_009518836__Norovirus_GII.17__552592

Identity

Accession:
YP_009518836 ↗
Protein ID:
VP1
Kingdom:
euk

Quality

83.3 mean pLDDT

Taxonomy

Orthornavirae› Pisuviricota› Pisoniviricetes› Picornavirales› Caliciviridae› Norovirus› Norovirus_GII.17

TaxID: 552592

Cluster

View cluster (17 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 50-215
PDB
Domain cluster: rep: structural_polyprotein__YP_009333175__Bastrovirus-like_virus_VietNam_Bat_17819_21__1906170__D141-305
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF00915.27 best Calici_coat 191.3 2.50e-56 100.0% 55.1%
PF00073.27 Rhv 34.1 3.00e-08 78.9% 57.3%
D2 medium residues 230-282_396-533
PDB
Domain cluster: rep: VP1__YP_009679035__Norovirus_GII_Hu_JP_2007_GII.P15_GII.15_Sapporo_HK299__1529918__D230-281_420-543
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF08435.18 best Calici_coat_C 251.7 9.40e-75 95.8% 62.6%
D3 medium residues 283-395
PDB
Domain cluster: rep: VP1_capsid_protein__YP_009679041__Norovirus_dog_GVI.1_HKU_Ca026F_2007_HKG__673457__D281-384
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF08435.18 best Calici_coat_C 67.8 1.50e-18 81.4% 38.3%
CATH (35)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6j0qA02 2.40.30.120 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses 0.93 87.0 8.91e-01 97.3% 100.0%
3q39B02 2.40.30.120 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses 0.92 87.0 8.87e-01 97.3% 100.0%
4qv2A02 2.40.30.120 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses 0.87 83.0 8.22e-01 100.0% 97.5%
2zl7A02 2.40.30.120 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses 0.87 67.0 7.46e-01 97.3% 100.0%
4rlzA02 2.40.30.120 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses 0.86 81.0 8.26e-01 97.3% 100.0%
5e6tA02 2.40.30.120 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses 0.86 69.0 7.54e-01 97.3% 100.0%
3lq6A02 2.40.30.120 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses 0.85 79.0 7.91e-01 97.3% 100.0%
4rdlA02 2.40.30.120 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Positive stranded ssRNA viruses 0.83 75.0 7.69e-01 97.3% 100.0%
3op1A02 2.40.30.30 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Riboflavin kinase-like 0.68 58.0 5.90e-01 100.0% 91.9%
1fuiA03 3.20.14.10 Alpha Beta › Alpha-Beta Barrel › L-fucose Isomerase; Chain A, domain 3 › L-fucose/L-arabinose isomerase, C-terminal 0.66 59.0 4.48e-01 95.6% 72.1%
3w1eA03 2.40.10.410 Mainly Beta › Beta Barrel › Thrombin, subunit H › FlgT, C-terminal domain 0.66 49.0 5.46e-01 91.2% 98.9%
2qcpX01 2.40.50.320 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Copper binding periplasmic protein CusF 0.63 35.0 4.21e-01 98.2% 82.7%
1n08A00 2.40.30.30 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Riboflavin kinase-like 0.61 51.0 4.66e-01 100.0% 68.2%
4n0rA03 2.60.40.3950 Mainly Beta › Sandwich › Immunoglobulin-like › 0.60 45.0 4.59e-01 95.6% 80.9%
4dyoA02 2.30.250.10 Mainly Beta › Roll › Aminopeptidase i, Domain 2 › Aminopeptidase i, Domain 2 0.60 52.0 4.84e-01 93.8% 100.0%
1vwxB02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.59 54.0 4.60e-01 100.0% 81.7%
1vq8B02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.58 53.0 5.00e-01 99.1% 89.8%
1a7sA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.58 40.0 4.05e-01 83.2% 71.4%
3rd4B00 2.40.50.660 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.58 36.0 4.18e-01 97.3% 86.6%
7ylrA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.57 49.0 5.04e-01 93.8% 100.0%
3buuB00 2.50.20.10 Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › Lipoprotein localisation LolA/LolB/LppX 0.57 40.0 3.22e-01 72.6% 94.5%
3s98A03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 37.0 4.04e-01 96.5% 84.9%
1si5H01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.54 43.0 4.24e-01 84.1% 100.0%
2zgcA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.54 42.0 4.09e-01 82.3% 96.0%
2vpaA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.54 43.0 3.55e-01 85.0% 63.7%
1xhnA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.54 42.0 3.75e-01 85.0% 75.3%
2eddA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 37.0 3.73e-01 95.6% 71.4%
2wstA00 2.60.90.10 Mainly Beta › Sandwich › Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) › Adenovirus pIV-related, attachment domain 0.53 46.0 3.98e-01 96.5% 75.6%
6rptC00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 39.0 3.92e-01 96.5% 81.2%
3hvnA01 3.90.840.10 Alpha Beta › Alpha-Beta Complex › HIV-1 Reverse Transcriptase; Chain A, domain 3 › Thiol-activated cytolysin superfamily/Thiol-activated cytolysin, alpha-beta domain 0.51 37.0 3.27e-01 76.1% 62.2%
1uenA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 37.0 3.65e-01 96.5% 70.4%
1wfoA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 35.0 3.66e-01 95.6% 77.9%
5fahA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.50 38.0 3.79e-01 89.4% 76.1%
1gvzA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.50 40.0 3.91e-01 89.4% 78.5%
5e55B02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 34.0 3.69e-01 96.5% 86.0%
ECOD (27)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2505866 1.2.1.4 ↗ beta barrels › cradle loop barrel › Capsid protein protrusion (P) domain › Capsid protein protrusion (P) domain › Calici_coat, Calici_coat_C 0.94 72.0 6.45e-01 78.8% 62.8%
2505880 1.2.1.2 ↗ beta barrels › cradle loop barrel › Capsid protein protrusion (P) domain › Capsid protein protrusion (P) domain › Calici_coat_C 0.94 74.0 6.66e-01 85.8% 63.0%
2505848 1.2.1.2 ↗ beta barrels › cradle loop barrel › Capsid protein protrusion (P) domain › Capsid protein protrusion (P) domain › Calici_coat_C 0.93 90.0 8.04e-01 100.0% 79.7%
2553941 10.2.1.43 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Calici_coat_C 0.92 89.0 6.17e-01 100.0% 36.4%
4881921 10.2.1.14 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) 0.86 81.0 5.72e-01 100.0% 36.7%
2505857 1.2.1.2 ↗ beta barrels › cradle loop barrel › Capsid protein protrusion (P) domain › Capsid protein protrusion (P) domain › Calici_coat_C 0.84 75.0 6.94e-01 100.0% 77.2%
2126884 10.2.1.43 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Calici_coat_C 0.84 80.0 5.60e-01 100.0% 49.8%
4881922 1.2.1.2 ↗ beta barrels › cradle loop barrel › Capsid protein protrusion (P) domain › Capsid protein protrusion (P) domain › Calici_coat_C 0.84 74.0 6.87e-01 100.0% 77.2%
1696469 10.2.1.43 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Calici_coat_C 0.82 76.0 5.48e-01 100.0% 37.9%
2171578 1.2.1.2 ↗ beta barrels › cradle loop barrel › Capsid protein protrusion (P) domain › Capsid protein protrusion (P) domain › Calici_coat_C 0.82 78.0 7.19e-01 99.1% 81.8%
4856093 10.2.1.43 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Calici_coat_C 0.81 73.0 7.14e-01 100.0% 89.9%
4872941 10.2.1.43 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Calici_coat_C 0.80 71.0 7.01e-01 93.8% 92.4%
1695947 10.2.1.14 ↗ beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) 0.80 72.0 5.08e-01 100.0% 34.7%
3740846 1.1.7.46 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › SMUBP-2_HCS1_1B 0.68 58.0 5.83e-01 95.6% 89.6%
3240679 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.66 60.0 5.28e-01 97.3% 69.4%
115 1.1.7.18 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Fucose_iso_C 0.66 58.0 4.55e-01 95.6% 76.3%
3703044 1.1.7.10 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Flavokinase 0.66 60.0 5.24e-01 99.1% 76.4%
3924486 2004.1.1.184 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_11 0.65 58.0 3.82e-01 100.0% 55.1%
4171511 1.1.7.10 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › Flavokinase 0.62 56.0 4.76e-01 100.0% 64.7%
3190862 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.62 54.0 5.29e-01 95.6% 100.0%
1108154 12.1.1.41 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › DUF5605 0.60 45.0 4.62e-01 95.6% 82.4%
5033844 71.1.1.8 ↗ beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › LolA_like 0.57 40.0 3.17e-01 72.6% 94.2%
3213122 4184.1.1.0 ↗ beta barrels › MFPT repeat › MFPT repeat › MFPT repeat 0.55 41.0 4.27e-01 95.6% 85.7%
3331566 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 40.0 4.01e-01 95.6% 83.5%
4003995 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.51 41.0 3.79e-01 88.5% 83.3%
3884372 11.1.1.711 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › FN3_IL27B_N 0.50 33.0 3.52e-01 89.4% 76.0%
3938968 10.32.1.4 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › EMP24_GP25L 0.50 35.0 3.56e-01 95.6% 72.2%