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3D_protein

Euk-Vir

Crohivirus_A

3D_protein__YP_009104398__Crohivirus_A__2169853

Identity

Accession:
YP_009104398 ↗
Protein ID:
3D_protein
Kingdom:
euk

Quality

95.6 mean pLDDT

Taxonomy

Orthornavirae› Pisuviricota› Pisoniviricetes› Picornavirales› Picornaviridae› Crohivirus› Crohivirus_A

TaxID: 2169853

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 385-469
PDB
Domain cluster: rep: putative_3D_RNA-dependent_RNA_polymerase__YP_009553719__tremovirus_B1__2058161__D405-481
CATH (26)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ra6A03 1.20.960.20 Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A › 0.83 77.0 7.70e-01 100.0% 98.9%
2ckwA04 1.20.960.20 Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A › 0.83 76.0 7.00e-01 100.0% 91.6%
3nkyA03 1.20.960.20 Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A › 0.82 58.0 6.23e-01 81.2% 86.3%
1khvA05 1.20.960.20 Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A › 0.81 75.0 7.14e-01 100.0% 100.0%
3h5xA04 1.20.960.20 Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A › 0.69 61.0 5.93e-01 98.8% 94.7%
5dllA05 1.25.50.10 Mainly Alpha › Alpha Horseshoe › Zincin-like fold › Peptidase M1, alanyl aminopeptidase, C-terminal domain 0.62 51.0 3.50e-01 92.9% 61.3%
2l1lB00 1.20.1440.250 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.60 47.0 4.15e-01 84.7% 69.3%
1eq1A00 1.20.120.20 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein 0.60 43.0 3.43e-01 74.1% 87.3%
6tblB01 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.59 48.0 4.42e-01 89.4% 99.1%
4oydB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.58 42.0 3.86e-01 77.6% 92.3%
4jxtA00 1.25.40.90 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.58 44.0 3.95e-01 96.5% 56.2%
4ksaA02 1.20.140.90 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Malonyl-CoA decarboxylase, oligemerization domain 0.57 40.0 3.54e-01 75.3% 81.0%
4a64A01 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.56 46.0 4.02e-01 90.6% 84.8%
5m9dA00 1.25.40.90 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.56 45.0 3.92e-01 90.6% 84.8%
4he8D00 1.20.120.1200 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ 0.55 38.0 3.08e-01 94.1% 37.5%
7zm7601 1.20.120.1200 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ 0.55 37.0 2.99e-01 92.9% 35.3%
3rkoF01 1.20.120.1200 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ 0.55 38.0 3.07e-01 92.9% 37.5%
6humG01 1.20.120.1200 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › NADH-ubiquinone/plastoquinone oxidoreductase chain 6, subunit NuoJ 0.55 38.0 3.12e-01 92.9% 38.7%
1i6zA00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.54 41.0 3.54e-01 80.0% 75.6%
1o0sA02 1.20.1370.30 Mainly Alpha › Up-down Bundle › Hemocyanin, N-terminal domain › 0.54 46.0 4.28e-01 95.3% 97.2%
3a8pA02 6.10.140.680 Special › Helix non-globular › Helix Hairpins › 0.54 46.0 4.20e-01 97.6% 95.6%
2vvwA00 1.10.437.20 Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › dsDNA poxvirus 0.53 38.0 3.21e-01 75.3% 71.3%
1u7kA00 1.10.375.10 Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein 0.52 41.0 3.66e-01 90.6% 92.4%
4q5nA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.52 41.0 3.84e-01 89.4% 82.1%
6q9jB02 1.20.1440.230 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › NADH-ubiquinone oxidoreductase 51kDa subunit, iron-sulphur binding domain 0.51 38.0 3.83e-01 81.2% 78.4%
4o6yB00 1.20.120.1770 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.51 40.0 3.18e-01 90.6% 94.8%
ECOD (35)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
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 0.84 78.0 7.45e-01 100.0% 88.7%
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 0.79 72.0 6.77e-01 100.0% 90.2%
3673084 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.70 55.0 4.26e-01 96.5% 38.9%
3339599 109.4.1.420 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR 0.70 54.0 4.39e-01 82.4% 48.4%
4974797 3352.1.1.0 ↗ alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain 0.67 57.0 3.73e-01 95.3% 51.6%
3438832 109.4.1.1308 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, PPR_2, PPR_3, TPR_24 0.63 53.0 3.41e-01 92.9% 25.8%
4593326 3651.1.1.1 ↗ alpha bundles › Translation initiation factor eIF-2B delta subunit N-terminal helical domain › Translation initiation factor eIF-2B delta subunit N-terminal helical domain › Translation initiation factor eIF-2B delta subunit N-terminal helical domain › IF-2B 0.63 49.0 4.20e-01 84.7% 88.6%
3497847 109.4.1.2736 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Importin_rep_4, Importin_rep_6, TPR_IPO5 0.63 50.0 3.07e-01 89.4% 26.0%
5020681 3352.1.1.0 ↗ alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain 0.63 51.0 3.27e-01 90.6% 42.0%
3971032 1051.1.1.1 ↗ alpha superhelices › Putative 3-oxoacyl-(acyl-carrier-protein) synthase N-terminal domain › Putative 3-oxoacyl-(acyl-carrier-protein) synthase N-terminal domain › Putative 3-oxoacyl-(acyl-carrier-protein) synthase N-terminal domain › HOASN 0.62 44.0 4.39e-01 75.3% 88.9%
3317357 109.4.1.420 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR 0.60 53.0 3.86e-01 97.6% 46.1%
3772926 611.3.1.13 ↗ alpha bundles › N-cbl like › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 › PF26718 0.60 49.0 4.35e-01 90.6% 97.6%
3299098 109.4.1.172 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › MMS19_C 0.60 47.0 3.83e-01 87.1% 70.0%
4828003 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.60 43.0 3.90e-01 77.6% 88.4%
3572779 3855.1.1.1 ↗ alpha arrays › Serum amyloid A-1 protein › Serum amyloid A-1 protein › Serum amyloid A-1 protein › SAA 0.60 49.0 4.54e-01 91.8% 86.4%
3263316 109.4.1.661 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › CNOT11 0.59 48.0 3.78e-01 87.1% 45.1%
4986595 3843.1.1.0 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K 0.59 40.0 3.94e-01 70.6% 92.6%
2721357 604.39.1.5 ↗ alpha bundles › Spectrin repeat-like › S-component of energy-coupling factor (ECF) transporters › S-component of energy-coupling factor (ECF) transporters › ECF_trnsprt 0.59 50.0 3.88e-01 98.8% 51.7%
4623297 109.4.1.70 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › CID 0.58 48.0 4.20e-01 92.9% 91.1%
3565390 109.4.1.2 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Arm 0.58 46.0 2.84e-01 88.2% 22.6%
3610681 109.4.1.83 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Suf 0.57 49.0 3.30e-01 100.0% 45.9%
5044204 3579.1.1.1 ↗ extended segments › NADH-quinone oxidoreductase subunit J › NADH-quinone oxidoreductase subunit J › NADH-quinone oxidoreductase subunit J › Oxidored_q3 0.57 38.0 3.16e-01 94.1% 39.3%
3598745 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.57 47.0 3.93e-01 92.9% 74.8%
4050574 192.17.1.11 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › UVR 0.57 41.0 4.28e-01 76.5% 90.7%
3709594 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.56 48.0 3.99e-01 96.5% 68.4%
3961 150.1.1.7 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › DUF892 0.56 42.0 3.47e-01 81.2% 89.4%
3596372 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.56 44.0 4.32e-01 88.2% 90.5%
3700350 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.56 44.0 3.95e-01 88.2% 93.6%
3751351 3796.1.1.0 ↗ alpha arrays › Iron-regulated surface determinant protein H linker domain › Iron-regulated surface determinant protein H linker domain › Iron-regulated surface determinant protein H linker domain 0.54 35.0 3.85e-01 80.0% 84.6%
3202400 622.1.1.20 ↗ alpha bundles › YvfG-like › HSC20 (HSCB), C-terminal oligomerisation domain › HSC20 (HSCB), C-terminal oligomerisation domain › Het-C 0.52 37.0 3.04e-01 76.5% 78.3%
3290726 633.6.1.2 ↗ alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like › ACOX 0.51 40.0 3.19e-01 94.1% 43.0%
4375226 3579.1.1.1 ↗ extended segments › NADH-quinone oxidoreductase subunit J › NADH-quinone oxidoreductase subunit J › NADH-quinone oxidoreductase subunit J › Oxidored_q3 0.51 37.0 3.07e-01 81.2% 42.6%
3843913 633.6.1.2 ↗ alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like › ACOX 0.50 41.0 3.15e-01 97.6% 40.0%
3283349 633.6.1.0 ↗ alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like 0.50 38.0 3.40e-01 94.1% 56.0%
3671721 633.6.1.2 ↗ alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like › ACOX 0.50 39.0 3.31e-01 94.1% 49.7%
D2 medium residues 1-14_94-227_269-299
PDB
Domain cluster: rep: RNA-dependent_RNA-polymerase_-RdRp-__YP_004429254__Grapevine_Bulgarian_latent_virus__748667__D66-229_264-320
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00680.26 best RdRP_1 74.6 9.30e-21 91.1% 28.0%
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5m38C00 3.30.1330.60 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › OmpA-like domain 0.58 30.0 3.71e-01 73.7% 77.2%
3oonA00 3.30.1330.60 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › OmpA-like domain 0.58 29.0 3.62e-01 73.2% 75.2%
1r1mA00 3.30.1330.60 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › OmpA-like domain 0.57 30.0 3.34e-01 73.7% 62.9%
1xw3A01 3.90.1530.10 Alpha Beta › Alpha-Beta Complex › Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain › Conserved hypothetical protein from pyrococcus furiosus pfu- 392566-001, ParB domain 0.56 28.0 3.65e-01 91.6% 87.5%
4rhaA00 3.30.1330.60 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › OmpA-like domain 0.54 29.0 3.27e-01 73.7% 67.2%
2d3o100 3.30.70.1050 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Trigger factor ribosome-binding domain 0.53 26.0 3.33e-01 77.7% 80.0%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5367 304.48.1.8 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1 0.90 87.0 6.55e-01 100.0% 78.6%
1173784 304.48.1.8 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1 0.87 84.0 6.38e-01 100.0% 78.0%
None — 0.86 84.0 6.35e-01 100.0% 78.1%
2541763 304.48.1.8 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1 0.86 83.0 6.24e-01 100.0% 78.4%
1875037 304.48.1.8 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1 0.82 76.0 5.79e-01 98.3% 75.8%
1279063 304.48.1.13 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Flavi_NS5 0.79 75.0 5.46e-01 100.0% 68.9%
4871000 304.48.1.8 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RdRP_1 0.67 63.0 5.43e-01 98.3% 93.2%
4882532 304.48.1.0 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.67 58.0 4.72e-01 92.2% 69.9%
4024117 101.1.2.366 ↗ alpha arrays › HTH › HTH › winged helix domain › DUF3161 0.54 27.0 3.57e-01 82.1% 90.0%
D3 medium residues 66-93_228-268_300-379
PDB
Domain cluster: rep: KR816341.1__AKQ06880.1__X__00021__D162-195_238-325
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00680.26 best RdRP_1 40.3 2.40e-10 56.4% 18.2%