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VP1

Euk-Vir

Rotavirus_A

VP1__YP_002302227__Rotavirus_A__28875

Identity

Accession:
YP_002302227 ↗
Protein ID:
VP1
Kingdom:
euk

Quality

63.4 mean pLDDT

Taxonomy

Orthornavirae› Duplornaviricota› Resentoviricetes› Reovirales› Sedoreoviridae› Rotavirus› Rotavirus_A

TaxID: 28875

Cluster

View cluster (29 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 236-335_616-689
PDB
Domain cluster: representative
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF02123.22 best RdRP_4 25.8 7.10e-06 52.9% 10.8%
PF02123.22 RdRP_4 30.1 3.60e-07 46.6% 10.5%
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2r7rA04 3.30.70.2480 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.64 53.0 5.64e-01 89.1% 94.9%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4969507 2003.1.2.40 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_oxidored 0.51 27.0 3.35e-01 71.3% 85.0%
D2 medium residues 1-97
PDB
D3 medium residues 134-235
PDB
D4 medium residues 336-386_450-491_506-597
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF02123.22 best RdRP_4 98.0 9.20e-28 73.5% 27.3%
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2r7rA05 1.10.357.80 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › 0.79 73.0 7.51e-01 97.3% 100.0%
4f0uA00 1.10.490.20 Mainly Alpha › Orthogonal Bundle › Globin-like › Phycocyanins 0.55 30.0 3.22e-01 76.2% 58.7%
2ib0A01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.54 36.0 4.15e-01 76.8% 92.6%
3fseB02 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.53 38.0 4.26e-01 73.5% 93.1%
4r42A01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.52 38.0 3.84e-01 73.5% 86.6%
7qocA01 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.52 29.0 2.98e-01 78.4% 52.9%
5ffdA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.52 36.0 4.18e-01 76.8% 97.1%
1f1mA00 1.20.120.240 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Lipoprotein, type 6 0.51 32.0 3.46e-01 80.5% 71.6%
1kn1B00 1.10.490.20 Mainly Alpha › Orthogonal Bundle › Globin-like › Phycocyanins 0.51 29.0 3.10e-01 83.8% 60.9%
5t3wA00 1.20.120.1160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.50 28.0 3.18e-01 90.3% 70.1%
1lkoA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.50 36.0 3.99e-01 73.5% 91.7%
1dpsA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.50 36.0 3.87e-01 73.5% 86.8%
ECOD (14)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
223786 304.48.1.16 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_4 0.86 81.0 6.54e-01 98.4% 76.8%
3510771 610.4.1.0 ↗ alpha arrays › ERP29 C domain-like › YqeY domain › YqeY domain 0.65 36.0 4.83e-01 85.9% 100.0%
3805784 109.4.1.3484 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR_1, E_motif 0.57 24.0 2.55e-01 71.4% 41.8%
3742220 109.4.1.307 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Tho2 0.55 32.0 2.78e-01 82.7% 34.8%
4932167 150.1.1.3 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Rubrerythrin 0.54 35.0 4.11e-01 75.7% 91.5%
3693968 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.54 31.0 3.32e-01 78.4% 64.4%
5050607 150.1.1.3 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Rubrerythrin 0.54 35.0 4.09e-01 75.7% 91.5%
3588872 601.1.1.11 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › EcsB 0.53 38.0 4.12e-01 88.6% 88.2%
4283593 150.1.1.3 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Rubrerythrin 0.53 35.0 4.07e-01 74.1% 91.9%
3951159 150.1.1.12 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › DUF4439 0.53 36.0 3.99e-01 75.7% 87.6%
3288395 150.1.1.12 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › DUF4439 0.52 35.0 4.06e-01 76.8% 92.6%
3607460 4967.1.1.0 ↗ alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases 0.52 39.0 3.70e-01 87.0% 64.1%
4512907 604.2.1.1 ↗ alpha bundles › Spectrin repeat-like › Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain › Succinate dehydrogenase/fumarate reductase flavoprotein C-terminal domain › Succ_DH_flav_C 0.51 23.0 2.66e-01 87.6% 55.9%
4981470 150.1.1.3 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Rubrerythrin 0.50 37.0 3.94e-01 76.8% 84.8%
D5 medium residues 387-449
PDB
D6 medium residues 692-760
PDB
D7 medium residues 761-860
PDB
D8 medium residues 861-927_994-1088
PDB
D9 medium residues 928-993
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF12289.14 best Rotavirus_VP1 116.3 2.10e-33 100.0% 20.9%
CATH (15)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2r7rA08 1.20.120.1400 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.97 92.0 8.28e-01 100.0% 76.7%
3ddhA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.62 45.0 4.30e-01 78.8% 95.1%
6cy5A01 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.61 47.0 4.25e-01 81.8% 76.4%
1v9mA01 1.10.132.50 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › ATP synthase (C/AC39) subunit, domain 3 0.61 47.0 3.96e-01 84.8% 89.6%
3q2eA00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.61 44.0 3.85e-01 78.8% 93.5%
2dflA01 1.10.150.20 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain 0.59 43.0 4.44e-01 95.5% 90.0%
5c9eB01 1.20.1280.80 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.57 47.0 4.45e-01 100.0% 77.0%
1y02A01 1.10.720.140 Mainly Alpha › Orthogonal Bundle › Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 › 0.57 37.0 3.52e-01 71.2% 56.4%
2l3nA00 1.10.1050.20 Mainly Alpha › Orthogonal Bundle › Ribosomal Protein S4 Delta 41; Chain A, domain 1 › 0.54 47.0 4.11e-01 100.0% 79.8%
5vyoD00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.54 46.0 3.42e-01 100.0% 40.4%
1b72A00 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.54 40.0 4.04e-01 90.9% 82.4%
1znnA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.54 44.0 3.05e-01 93.9% 40.0%
3qhbA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.52 44.0 3.23e-01 93.9% 77.1%
2remB00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.52 44.0 3.29e-01 100.0% 42.2%
3w5mA05 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.52 42.0 2.75e-01 95.5% 23.7%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1173790 4962.1.1.3 ↗ alpha complex topology › C-terminal additional helical subdomain in reovirus polymerase lambda3 › C-terminal additional helical subdomain in reovirus polymerase lambda3 › C-terminal additional helical subdomain in reovirus polymerase lambda3 › Rotavirus_VP1 0.97 92.0 5.63e-01 100.0% 20.1%
5023052 5060.1.1.0 ↗ alpha bundles › V-type ATP synthase subunit C › V-type ATP synthase subunit C › V-type ATP synthase subunit C 0.71 51.0 4.96e-01 77.3% 100.0%
4013869 2485.1.1.10 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › DSBA 0.63 49.0 3.57e-01 100.0% 28.5%
3268699 198.1.1.0 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.61 48.0 4.75e-01 95.5% 82.2%
3168643 592.1.1.2 ↗ alpha arrays › PWI domain-like › PWI domain › PWI domain › Helicase_PWI 0.60 49.0 4.52e-01 98.5% 74.7%
5012322 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.60 50.0 3.69e-01 100.0% 83.5%
3495504 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.59 41.0 4.50e-01 89.4% 100.0%
3944622 101.1.4.0 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like 0.58 43.0 4.13e-01 83.3% 88.7%
3560402 101.1.1.36 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Homeobox_KN 0.57 40.0 4.09e-01 93.9% 80.0%
3653578 206.1.1.7 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › PI3_PI4_kinase 0.56 42.0 2.66e-01 78.8% 56.9%
3889817 101.1.1.1 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Homeodomain 0.55 43.0 4.12e-01 93.9% 73.8%
3882807 101.1.1.1 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Homeodomain 0.55 41.0 3.91e-01 95.5% 68.8%
4455972 102.1.1.0 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like 0.55 45.0 3.54e-01 98.5% 93.1%
5039569 2485.1.1.10 ↗ a+b three layers › Thioredoxin-like › Thioredoxin-like › Thioredoxin-like › DSBA 0.55 47.0 3.39e-01 100.0% 68.6%
4319187 101.1.1.1 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Homeodomain 0.53 39.0 3.71e-01 89.4% 64.7%
3793622 6126.1.1.1 ↗ alpha bundles › Helical domain in EHD2 › Helical domain in EHD2 › Helical domain in EHD2 › DUF5600 0.53 44.0 3.49e-01 95.5% 46.2%
3218285 101.1.1.1 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Homeodomain 0.52 42.0 3.83e-01 93.9% 67.4%