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capsid_protein

Euk-Vir

Vesivirus_ferret_badger_JX12_China_2012

capsid_protein__YP_009140469__Vesivirus_ferret_badger_JX12_China_2012__1615583

Identity

Accession:
YP_009140469 ↗
Protein ID:
capsid_protein
Kingdom:
euk

Quality

59.9 mean pLDDT

Taxonomy

Orthornavirae› Pisuviricota› Pisoniviricetes› Picornavirales› Caliciviridae› Vesivirus› Vesivirus_ferret_badger/JX12/China/2012

TaxID: 1615583

Cluster

View cluster (4 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 36-145
PDB
D2 high residues 200-360
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 249.6 4.40e-74 100.0% 55.1%
PF00073.27 Rhv 30.5 3.70e-07 80.1% 67.2%
D3 high residues 376-415_562-676
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
PF00915.27 best Calici_coat 29.2 6.20e-07 36.1% 16.8%
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3bqjA01 2.40.510.10 Mainly Beta › Beta Barrel › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Positive stranded ssRNA viruses 0.76 70.0 6.48e-01 100.0% 93.3%
4p25D01 2.40.510.10 Mainly Beta › Beta Barrel › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Positive stranded ssRNA viruses 0.75 70.0 6.49e-01 100.0% 90.7%
6xw5A01 2.40.510.10 Mainly Beta › Beta Barrel › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Positive stranded ssRNA viruses 0.74 67.0 6.47e-01 97.4% 99.4%
2greF02 2.40.30.40 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Peptidase M42, domain 2 0.61 33.0 4.34e-01 97.4% 100.0%
1ok0A00 2.60.40.20 Mainly Beta › Sandwich › Immunoglobulin-like › Alpha-amylase inhibitor 0.61 29.0 3.89e-01 98.1% 89.2%
3kl9A02 2.40.30.40 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Peptidase M42, domain 2 0.61 31.0 4.22e-01 91.0% 100.0%
3fqmA01 2.20.25.210 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › Hepatitis C NS5A, domain 1B 0.60 24.0 3.68e-01 85.2% 91.8%
2bseA00 2.60.40.1830 Mainly Beta › Sandwich › Immunoglobulin-like › Phage tail base-plate Siphoviridae RBP, head domain 0.58 36.0 4.31e-01 98.7% 90.7%
2f0cA02 2.60.40.1830 Mainly Beta › Sandwich › Immunoglobulin-like › Phage tail base-plate Siphoviridae RBP, head domain 0.58 36.0 4.25e-01 98.7% 91.3%
4mboA01 2.60.40.1280 Mainly Beta › Sandwich › Immunoglobulin-like › 0.57 32.0 3.26e-01 98.7% 53.0%
1yloE02 2.40.30.40 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Peptidase M42, domain 2 0.57 32.0 4.13e-01 98.1% 100.0%
5mj6A03 2.60.40.1910 Mainly Beta › Sandwich › Immunoglobulin-like › 0.57 29.0 3.75e-01 98.7% 90.0%
1mrzB02 2.40.30.30 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Riboflavin kinase-like 0.57 30.0 3.49e-01 100.0% 68.8%
3v76A02 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.56 28.0 3.49e-01 86.5% 77.8%
3p42A03 3.10.560.10 Alpha Beta › Roll › Outer membrane lipoprotein wza fold like › Outer membrane lipoprotein wza domain like 0.56 27.0 3.75e-01 96.1% 94.6%
1y6kR02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 30.0 3.59e-01 100.0% 82.5%
2jvuA00 2.60.40.2290 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 30.0 3.59e-01 99.4% 85.7%
2j5uA02 2.40.10.340 Mainly Beta › Beta Barrel › Thrombin, subunit H › Rod shape-determining protein MreC, domain 1 0.52 28.0 3.62e-01 96.8% 94.0%
2fsdA00 2.60.40.2460 Mainly Beta › Sandwich › Immunoglobulin-like › Phage bIL170 RBP, head domain 0.51 34.0 3.90e-01 98.7% 94.5%
ECOD (22)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
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 0.77 71.0 5.60e-01 100.0% 94.5%
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 0.74 68.0 5.38e-01 100.0% 92.7%
4958378 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.72 30.0 3.97e-01 87.1% 69.4%
4959054 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.69 29.0 3.88e-01 87.7% 70.6%
4890345 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.66 34.0 4.46e-01 98.7% 89.4%
4080130 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.66 33.0 4.53e-01 99.4% 98.7%
961561 5092.1.1.4 ↗ beta sandwiches › Domain in virus attachment proteins › Domain in virus attachment proteins › Domain in virus attachment proteins › Caudo_bapla_RBP 0.65 36.0 4.29e-01 98.7% 80.6%
4083044 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.64 32.0 4.36e-01 97.4% 96.0%
4047081 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.64 31.0 4.05e-01 100.0% 83.5%
5076995 1.1.7.17 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › ATP-synt_ab_N 0.63 33.0 4.35e-01 100.0% 96.2%
4943366 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.62 33.0 4.19e-01 98.7% 90.6%
1348621 221.11.1.1 ↗ a+b two layers › beta-Grasp › beta-grasp fold domain in probable beta-lactamase › beta-grasp fold domain in probable beta-lactamase › DUF4888 0.61 31.0 4.15e-01 96.8% 96.0%
5040173 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.60 33.0 3.80e-01 100.0% 71.7%
4992171 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.58 26.0 3.79e-01 98.7% 96.9%
4946128 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 35.0 3.91e-01 100.0% 78.3%
3270183 11.1.1.843 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF7034 0.56 35.0 3.74e-01 99.4% 70.4%
4147155 11.22.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Dispersin › Dispersin 0.56 32.0 3.97e-01 100.0% 94.4%
3243970 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.55 34.0 4.10e-01 99.4% 96.0%
3972951 1.1.7.88 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › PF25963 0.54 28.0 3.64e-01 98.7% 96.0%
4299010 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.53 31.0 3.71e-01 99.4% 89.5%
3786521 1.1.7.46 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › SMUBP-2_HCS1_1B 0.53 34.0 3.87e-01 100.0% 87.0%
3289752 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.52 34.0 3.87e-01 97.4% 91.8%
D4 high residues 426-470_483-552
PDB