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VP1
Euk-VirNorovirus_GI
VP1__NP_056821__Norovirus_GI__122928
Identity
- Accession:
- NP_056821 ↗
- Protein ID:
- VP1
- Kingdom:
- euk
Quality
75.1
mean pLDDT
Taxonomy
Orthornavirae›
Pisuviricota›
Pisoniviricetes›
Picornavirales›
Caliciviridae›
Norovirus›
Norovirus_GI
TaxID: 122928
Cluster
Singleton — not in a non-trivial cluster
3D Structure
Domains
high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.
D1
high
residues 54-219
Domain cluster:
rep: structural_polyprotein__YP_009333175__Bastrovirus-like_virus_VietNam_Bat_17819_21__1906170__D141-305
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00915.27 best | Calici_coat | 268.0 | 1.10e-79 | 100.0% | 55.1% |
| PF00073.27 | Rhv | 38.2 | 1.70e-09 | 72.9% | 49.1% |
D2
medium
residues 231-400
Domain cluster:
representative
Pfam (2)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF08435.18 best | Calici_coat_C | 86.1 | 3.70e-24 | 58.8% | 45.6% |
| PF00915.27 | Calici_coat | 48.7 | 7.10e-13 | 38.2% | 19.9% |
CATH (9)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2gk6A02 | 2.40.30.230 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › | 0.60 | 31.0 | 4.22e-01 | 77.1% | 100.0% |
| 1tdqA02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.58 | 29.0 | 3.73e-01 | 78.8% | 85.6% |
| 3qt2B03 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.56 | 29.0 | 3.62e-01 | 86.5% | 82.7% |
| 1x5fA00 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.56 | 30.0 | 3.49e-01 | 89.4% | 71.7% |
| 4rt0A00 | 2.40.10.220 | Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains | 0.54 | 29.0 | 3.49e-01 | 74.1% | 78.9% |
| 2dn7A00 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.53 | 28.0 | 3.41e-01 | 84.1% | 78.5% |
| 4g1vA02 | 2.40.30.10 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors | 0.52 | 36.0 | 4.21e-01 | 82.9% | 100.0% |
| 1n26A03 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.52 | 29.0 | 3.46e-01 | 87.1% | 82.7% |
| 1uc6A00 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.51 | 29.0 | 3.44e-01 | 83.5% | 82.6% |
ECOD (25)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T 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 | 0.84 | 63.0 | 6.79e-01 | 77.1% | 100.0% |
| 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) | 0.83 | 78.0 | 6.32e-01 | 100.0% | 60.7% |
| 2505880 | 1.2.1.2 ↗ | beta barrels › cradle loop barrel › Capsid protein protrusion (P) domain › Capsid protein protrusion (P) domain › Calici_coat_C | 0.83 | 64.0 | 6.88e-01 | 79.4% | 100.0% |
| 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) | 0.83 | 78.0 | 6.24e-01 | 100.0% | 58.2% |
| 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 | 77.0 | 6.29e-01 | 100.0% | 62.1% |
| 2127918 | 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 | 76.0 | 6.27e-01 | 100.0% | 58.7% |
| 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 | 0.81 | 76.0 | 6.09e-01 | 100.0% | 59.1% |
| 2505848 | 1.2.1.2 ↗ | beta barrels › cradle loop barrel › Capsid protein protrusion (P) domain › Capsid protein protrusion (P) domain › Calici_coat_C | 0.80 | 59.0 | 6.32e-01 | 75.9% | 100.0% |
| 2505857 | 1.2.1.2 ↗ | beta barrels › cradle loop barrel › Capsid protein protrusion (P) domain › Capsid protein protrusion (P) domain › Calici_coat_C | 0.80 | 59.0 | 6.54e-01 | 75.9% | 100.0% |
| 4881922 | 1.2.1.2 ↗ | beta barrels › cradle loop barrel › Capsid protein protrusion (P) domain › Capsid protein protrusion (P) domain › Calici_coat_C | 0.75 | 54.0 | 5.95e-01 | 72.4% | 97.8% |
| 2171578 | 1.2.1.2 ↗ | beta barrels › cradle loop barrel › Capsid protein protrusion (P) domain › Capsid protein protrusion (P) domain › Calici_coat_C | 0.73 | 52.0 | 5.70e-01 | 72.4% | 98.5% |
| 3784576 | 1.1.7.0 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C | 0.63 | 37.0 | 4.61e-01 | 78.8% | 94.3% |
| 5073223 | 1.1.7.0 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C | 0.62 | 31.0 | 4.17e-01 | 80.0% | 92.9% |
| 3565481 | 11.1.1.2 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 | 0.59 | 32.0 | 3.88e-01 | 80.6% | 82.9% |
| 3744112 | 1.1.7.7 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 | 0.58 | 37.0 | 4.51e-01 | 82.9% | 100.0% |
| 4463780 | 1.1.5.25 ↗ | beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › PilZ | 0.56 | 31.0 | 3.73e-01 | 72.9% | 80.9% |
| 3172185 | 1.1.7.0 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C | 0.56 | 34.0 | 4.15e-01 | 79.4% | 92.7% |
| 5041801 | 4.15.1.0 ↗ | beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like | 0.56 | 29.0 | 3.99e-01 | 84.1% | 100.0% |
| 4270536 | 1.1.7.96 ↗ | beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FIST_C | 0.53 | 32.0 | 3.96e-01 | 77.1% | 99.0% |
| 5001346 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.53 | 29.0 | 3.31e-01 | 85.3% | 70.4% |
| 3762946 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.52 | 31.0 | 3.65e-01 | 87.6% | 87.3% |
| 3360847 | 10.32.1.104 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › VIR_N | 0.51 | 30.0 | 3.42e-01 | 88.2% | 76.8% |
| 1851176 | 5092.1.1.0 ↗ | beta sandwiches › Domain in virus attachment proteins › Domain in virus attachment proteins › Domain in virus attachment proteins | 0.51 | 39.0 | 4.27e-01 | 78.8% | 100.0% |
| 3799348 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.51 | 30.0 | 3.45e-01 | 80.0% | 79.2% |
| 4942527 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.50 | 27.0 | 3.38e-01 | 78.8% | 86.0% |
D3
medium
residues 401-518
Domain cluster:
rep: putative_67.3_kDa_coat_protein__YP_009551900__Nephila_clavipes_virus_2__2108205__D481-595
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF08435.18 best | Calici_coat_C | 195.3 | 1.60e-57 | 100.0% | 51.3% |
CATH (18)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 4p25D01 | 2.40.510.10 | Mainly Beta › Beta Barrel › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Positive stranded ssRNA viruses | 0.92 | 87.0 | 7.09e-01 | 99.2% | 59.3% |
| 6xw5A01 | 2.40.510.10 | Mainly Beta › Beta Barrel › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Positive stranded ssRNA viruses | 0.92 | 81.0 | 6.95e-01 | 91.5% | 63.6% |
| 3bqjA01 | 2.40.510.10 | Mainly Beta › Beta Barrel › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Positive stranded ssRNA viruses | 0.90 | 86.0 | 7.00e-01 | 98.3% | 60.0% |
| 2x9zA02 | 2.60.40.1140 | Mainly Beta › Sandwich › Immunoglobulin-like › Collagen-binding surface protein Cna, B-type domain | 0.60 | 36.0 | 3.68e-01 | 72.0% | 61.9% |
| 6fwvA01 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.60 | 32.0 | 3.66e-01 | 76.3% | 67.8% |
| 4b3fX02 | 2.40.30.270 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › | 0.59 | 37.0 | 3.98e-01 | 81.4% | 74.5% |
| 4g5aA00 | 2.60.40.3080 | Mainly Beta › Sandwich › Immunoglobulin-like › | 0.57 | 32.0 | 3.48e-01 | 73.7% | 63.6% |
| 1r3fA02 | 2.30.130.10 | Mainly Beta › Roll › Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 › PUA domain | 0.56 | 25.0 | 3.18e-01 | 86.4% | 69.2% |
| 2h41A00 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.56 | 33.0 | 3.62e-01 | 74.6% | 70.5% |
| 3tesA00 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.56 | 33.0 | 3.62e-01 | 75.4% | 71.3% |
| 1owwA00 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.56 | 34.0 | 3.69e-01 | 74.6% | 74.2% |
| 3sd2A01 | 2.60.40.3080 | Mainly Beta › Sandwich › Immunoglobulin-like › | 0.53 | 29.0 | 3.45e-01 | 73.7% | 79.2% |
| 2ibgA02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.52 | 33.0 | 3.49e-01 | 74.6% | 71.6% |
| 7sf2A02 | 2.60.40.10 | Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins | 0.52 | 33.0 | 3.57e-01 | 75.4% | 79.6% |
| 1eotA00 | 2.40.50.40 | Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › | 0.51 | 22.0 | 2.74e-01 | 86.4% | 62.2% |
| 1go4A00 | 3.30.900.10 | Alpha Beta › 2-Layer Sandwich › Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A › HORMA domain | 0.51 | 43.0 | 3.73e-01 | 95.8% | 93.9% |
| 6v93E01 | 3.30.900.10 | Alpha Beta › 2-Layer Sandwich › Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A › HORMA domain | 0.51 | 44.0 | 3.75e-01 | 96.6% | 100.0% |
| 4g1vA02 | 2.40.30.10 | Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors | 0.50 | 40.0 | 4.04e-01 | 85.6% | 89.0% |
ECOD (30)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 2127918 | 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 | 0.93 | 88.0 | 6.34e-01 | 98.3% | 69.4% |
| 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) | 0.93 | 89.0 | 6.24e-01 | 98.3% | 38.7% |
| 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) | 0.92 | 89.0 | 6.26e-01 | 100.0% | 39.2% |
| 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 | 0.92 | 89.0 | 6.23e-01 | 100.0% | 38.7% |
| 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 | 0.91 | 83.0 | 5.91e-01 | 95.8% | 37.9% |
| 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 | 0.91 | 88.0 | 6.17e-01 | 100.0% | 68.5% |
| 4888112 | 1.2.1.2 ↗ | beta barrels › cradle loop barrel › Capsid protein protrusion (P) domain › Capsid protein protrusion (P) domain › Calici_coat_C | 0.80 | 65.0 | 5.58e-01 | 84.7% | 69.9% |
| 3283730 | 11.1.4.23 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › CarboxypepD_reg | 0.62 | 32.0 | 3.75e-01 | 74.6% | 68.2% |
| 3717225 | 221.1.1.0 ↗ | a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like | 0.60 | 40.0 | 4.25e-01 | 74.6% | 79.0% |
| 3630663 | 11.1.1.2 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 | 0.60 | 35.0 | 3.82e-01 | 74.6% | 69.0% |
| 4930614 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.56 | 34.0 | 3.97e-01 | 74.6% | 87.5% |
| 3858825 | 11.1.1.2 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 | 0.56 | 33.0 | 3.66e-01 | 75.4% | 71.6% |
| 3815461 | 11.1.4.99 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › PF30918 | 0.55 | 35.0 | 3.57e-01 | 76.3% | 62.5% |
| 3396187 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.55 | 34.0 | 3.83e-01 | 75.4% | 81.1% |
| 3812521 | 11.1.4.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like | 0.55 | 34.0 | 3.57e-01 | 77.1% | 66.4% |
| 3588235 | 11.1.4.36 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › SpaA | 0.54 | 33.0 | 3.58e-01 | 74.6% | 72.0% |
| 4054625 | 10.32.1.0 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like | 0.54 | 37.0 | 3.33e-01 | 71.2% | 85.3% |
| 4592291 | 11.1.1.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like | 0.53 | 35.0 | 3.48e-01 | 75.4% | 60.8% |
| 3868228 | 355.1.1.2 ↗ | few secondary structure elements › Trefoil/Plexin domain-like › Trefoil/Plexin domain-like › Trefoil/Plexin domain-like › PSI | 0.53 | 31.0 | 3.05e-01 | 73.7% | 50.4% |
| 3325410 | 11.1.4.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like | 0.52 | 34.0 | 3.46e-01 | 77.1% | 65.8% |
| 3273867 | 221.1.1.4 ↗ | a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PB1 | 0.52 | 30.0 | 3.39e-01 | 74.6% | 76.5% |
| 3994648 | 11.1.7.0 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › PEBP-like | 0.52 | 40.0 | 3.30e-01 | 83.9% | 70.0% |
| 3789405 | 859.1.1.0 ↗ | a+b two layers › The spindle assembly checkpoint protein mad2 › The spindle assembly checkpoint protein mad2 › The spindle assembly checkpoint protein mad2 | 0.52 | 45.0 | 3.71e-01 | 99.2% | 100.0% |
| 3178394 | 10.32.1.175 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › Rax2_3 | 0.51 | 36.0 | 3.19e-01 | 72.9% | 82.9% |
| 3808258 | 11.1.4.99 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › PF30918 | 0.51 | 32.0 | 3.19e-01 | 75.4% | 60.0% |
| 3205804 | 859.1.1.1 ↗ | a+b two layers › The spindle assembly checkpoint protein mad2 › The spindle assembly checkpoint protein mad2 › The spindle assembly checkpoint protein mad2 › HORMA | 0.51 | 44.0 | 3.71e-01 | 95.8% | 90.7% |
| 3937632 | 859.1.1.0 ↗ | a+b two layers › The spindle assembly checkpoint protein mad2 › The spindle assembly checkpoint protein mad2 › The spindle assembly checkpoint protein mad2 | 0.51 | 42.0 | 3.73e-01 | 90.7% | 92.6% |
| 2807188 | 11.1.1.14 ↗ | beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Glyco_hydro_2 | 0.51 | 33.0 | 3.53e-01 | 76.3% | 78.1% |
| 3419976 | 10.32.1.0 ↗ | beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like | 0.51 | 30.0 | 3.44e-01 | 76.3% | 80.0% |
| 3721128 | 859.1.1.1 ↗ | a+b two layers › The spindle assembly checkpoint protein mad2 › The spindle assembly checkpoint protein mad2 › The spindle assembly checkpoint protein mad2 › HORMA | 0.50 | 44.0 | 3.58e-01 | 100.0% | 100.0% |