←Back to structures

3D_protein

Euk-Vir

Rhimavirus_A

3D_protein__YP_009553696__Rhimavirus_A__2218594

Identity

Accession:
YP_009553696 ↗
Protein ID:
3D_protein
Kingdom:
euk

Quality

93.7 mean pLDDT

Taxonomy

Orthornavirae› Pisuviricota› Pisoniviricetes› Picornavirales› Picornaviridae› Rhimavirus_A

TaxID: 2218594

Cluster

View cluster (450 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 386-466
PDB
Domain cluster: rep: putative_3D_RNA-dependent_RNA_polymerase__YP_009553719__tremovirus_B1__2058161__D405-481
CATH (16)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ra6A03 1.20.960.20 Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A › 0.90 83.0 8.06e-01 97.5% 93.1%
3nkyA03 1.20.960.20 Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A › 0.89 70.0 7.36e-01 85.2% 90.4%
1khvA05 1.20.960.20 Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A › 0.77 67.0 6.36e-01 96.3% 96.9%
3h5xA04 1.20.960.20 Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A › 0.67 57.0 5.47e-01 95.1% 91.6%
4ksaA02 1.20.140.90 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Malonyl-CoA decarboxylase, oligemerization domain 0.64 47.0 3.96e-01 77.8% 83.9%
1elkA00 1.25.40.90 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.64 44.0 3.65e-01 72.8% 47.7%
2b6cA01 1.20.1660.10 Mainly Alpha › Up-down Bundle › ARM repeat fold › Hypothetical protein (EF3068) 0.64 47.0 4.22e-01 79.0% 62.9%
2b6cA02 1.25.40.290 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › ARM repeat domains 0.60 43.0 4.08e-01 75.3% 69.1%
1ks8A00 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.57 48.0 3.14e-01 100.0% 59.1%
3qqaA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.55 48.0 4.05e-01 100.0% 84.4%
1b1uA00 1.10.110.10 Mainly Alpha › Orthogonal Bundle › Hydrophobic Seed Protein › Plant lipid-transfer and hydrophobic proteins 0.55 39.0 3.51e-01 75.3% 86.3%
1fftC00 1.20.120.80 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c oxidase, subunit III, four-helix bundle 0.54 37.0 2.92e-01 70.4% 55.7%
5djsA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.54 40.0 3.31e-01 77.8% 46.9%
4ed9A01 3.40.50.10540 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Crotonobetainyl-coa:carnitine coa-transferase; domain 1 0.52 43.0 2.96e-01 90.1% 54.2%
3cqyB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.52 41.0 3.26e-01 88.9% 86.4%
4jz8B00 3.40.1160.10 Alpha Beta › 3-Layer(aba) Sandwich › Carbamate kinase › Acetylglutamate kinase-like 0.50 40.0 2.76e-01 90.1% 45.0%
ECOD (27)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2541767 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 0.96 91.0 8.47e-01 98.8% 87.6%
2390376 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 0.91 82.0 7.43e-01 100.0% 74.8%
1519288 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 0.90 85.0 7.95e-01 100.0% 85.6%
1147677 4967.1.1.2 ↗ 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 › RdRP_1 0.86 75.0 7.33e-01 98.8% 87.4%
3092371 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 0.82 74.0 6.81e-01 98.8% 87.3%
3779 4967.1.1.2 ↗ 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 › RdRP_1 0.78 69.0 6.25e-01 97.5% 88.8%
3412719 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.70 50.0 4.68e-01 75.3% 72.0%
3875410 109.4.1.893 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › UTP6_C 0.68 50.0 3.91e-01 77.8% 40.6%
3667435 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.68 47.0 4.16e-01 72.8% 50.8%
3823526 109.4.1.1282 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, PPR_2, TPR_24 0.67 50.0 3.41e-01 79.0% 23.9%
3826382 109.4.1.883 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR+PPR_2 0.67 48.0 4.25e-01 76.5% 78.3%
4952332 191.1.1.0 ↗ alpha bundles › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain › Tetracyclin repressor-like, C-terminal domain 0.65 49.0 4.25e-01 81.5% 83.8%
3452875 109.4.1.420 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR 0.65 49.0 3.71e-01 80.2% 49.5%
3510931 109.4.1.70 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › CID 0.65 52.0 3.99e-01 90.1% 43.0%
3810355 109.4.1.883 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR+PPR_2 0.61 49.0 3.54e-01 88.9% 66.1%
3820547 109.4.1.420 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR 0.61 44.0 3.76e-01 77.8% 48.6%
3716855 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.61 46.0 3.04e-01 82.7% 30.9%
3301232 109.4.1.1258 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, PPR_2 0.60 45.0 3.88e-01 79.0% 50.8%
3668753 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.59 43.0 3.74e-01 79.0% 51.9%
3676589 4198.1.1.0 ↗ alpha arrays › TerB-like › TerB-like › TerB-like 0.59 47.0 3.94e-01 87.7% 75.7%
5023700 608.1.1.1 ↗ alpha arrays › AhpD-like › AhpD-like › AhpD-like › CMD 0.59 42.0 4.09e-01 76.5% 87.4%
3356191 109.4.1.883 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR+PPR_2 0.59 47.0 3.53e-01 88.9% 75.3%
3380155 109.4.1.1260 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, PPR_long 0.59 47.0 3.00e-01 90.1% 39.3%
3649717 109.4.1.1280 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_long 0.58 45.0 3.62e-01 85.2% 77.1%
4946417 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.56 44.0 3.36e-01 90.1% 95.9%
3681529 109.4.1.1334 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_3, PPR_long 0.56 45.0 2.96e-01 93.8% 82.2%
3481568 3998.1.1.1 ↗ alpha arrays › Peptidase inhibitors family I29 › Peptidase inhibitors family I29 › Peptidase inhibitors family I29 › Inhibitor_I29 0.51 31.0 3.26e-01 100.0% 68.6%
D2 medium residues 1-69_84-183_264-284
PDB
Domain cluster: rep: NIb__YP_009221991__Jasmine_virus_T__1775963__D1-51_64-80_112-210_276-312
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00680.26 best RdRP_1 40.1 2.80e-10 77.4% 23.3%
D3 medium residues 70-83_184-202_242-263
PDB
Domain cluster: representative
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1iurA01 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.58 50.0 4.86e-01 98.2% 96.8%
4ex8A00 3.40.1790.10 Alpha Beta › 3-Layer(aba) Sandwich › Indigoidine synthase fold › Indigoidine synthase domain 0.57 40.0 2.50e-01 74.5% 31.9%
5c8aA01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.55 47.0 4.26e-01 98.2% 82.1%
3bgeA01 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.53 36.0 3.06e-01 70.9% 54.2%
1q1vA00 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.52 43.0 4.06e-01 98.2% 75.7%
2qffA00 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.51 35.0 3.25e-01 72.7% 83.8%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4132742 7549.1.1.1 ↗ a/b three-layered sandwiches › Indigoidine synthase A-like (Pfam 04227) › Indigoidine synthase A-like (Pfam 04227) › Indigoidine synthase A-like (Pfam 04227) › Indigoidine_A 0.58 40.0 2.51e-01 72.7% 27.0%
D4 medium residues 203-241_285-385
PDB
Domain cluster: rep: RNA_dependent_RNA_polymerase__YP_529897__Newbury_agent_1__331642__D58-79_192-241_281-399
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF02123.22 best RdRP_4 23.1 4.60e-05 79.3% 15.5%
PF00680.26 RdRP_1 53.1 3.20e-14 72.1% 23.1%