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3D

Euk-Vir

Chicken_picornavirus_4

3D__YP_009055035__Chicken_picornavirus_4__1534547

Identity

Accession:
YP_009055035 ↗
Protein ID:
3D
Kingdom:
euk

Quality

95.2 mean pLDDT

Taxonomy

Orthornavirae› Pisuviricota› Pisoniviricetes› Picornavirales› Picornaviridae› Chicken_picornavirus_4

TaxID: 1534547

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 399-469
PDB
Domain cluster: rep: putative_3D_RNA-dependent_RNA_polymerase__YP_009553719__tremovirus_B1__2058161__D405-481
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3nkyA03 1.20.960.20 Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A › 0.91 75.0 7.42e-01 95.8% 83.6%
1ra6A03 1.20.960.20 Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A › 0.88 82.0 7.58e-01 100.0% 80.5%
1khvA05 1.20.960.20 Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A › 0.78 71.0 6.34e-01 100.0% 86.6%
2ckwA04 1.20.960.20 Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A › 0.77 69.0 6.03e-01 100.0% 82.2%
5wp3B00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.71 50.0 4.45e-01 74.6% 85.3%
3h5xA04 1.20.960.20 Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A › 0.69 61.0 5.58e-01 100.0% 83.2%
4hd1A00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.67 47.0 3.22e-01 74.6% 40.7%
1t9kA01 1.20.120.420 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › translation initiation factor eif-2b, domain 1 0.64 55.0 4.50e-01 100.0% 75.0%
1ks8A00 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.64 49.0 3.11e-01 88.7% 35.8%
4jxtA00 1.25.40.90 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.63 53.0 4.48e-01 98.6% 56.2%
2b6cA01 1.20.1660.10 Mainly Alpha › Up-down Bundle › ARM repeat fold › Hypothetical protein (EF3068) 0.63 51.0 4.46e-01 94.4% 62.1%
3rjtA00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.62 51.0 3.68e-01 91.5% 62.1%
3d3oA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.62 52.0 3.94e-01 95.8% 46.6%
3dciA00 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.61 52.0 3.83e-01 100.0% 48.3%
5nl6B01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.61 45.0 3.78e-01 78.9% 81.0%
4aidA02 1.10.10.400 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Polyribonucleotide nucleotidyltransferase, RNA-binding domain 0.61 43.0 4.16e-01 76.1% 90.2%
2ganA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.60 47.0 3.70e-01 84.5% 85.4%
4xymC03 3.40.50.261 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Succinyl-CoA synthetase domains 0.57 48.0 3.72e-01 95.8% 51.5%
3qqaA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.57 47.0 3.93e-01 98.6% 76.6%
2pqrA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.57 44.0 4.06e-01 85.9% 66.7%
4jz8B00 3.40.1160.10 Alpha Beta › 3-Layer(aba) Sandwich › Carbamate kinase › Acetylglutamate kinase-like 0.57 46.0 3.14e-01 95.8% 63.0%
1b1uA00 1.10.110.10 Mainly Alpha › Orthogonal Bundle › Hydrophobic Seed Protein › Plant lipid-transfer and hydrophobic proteins 0.56 44.0 3.88e-01 90.1% 87.2%
3t9jA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.56 42.0 3.42e-01 83.1% 95.1%
1udxA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.54 46.0 3.57e-01 100.0% 83.9%
4gmqA00 1.10.8.840 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ribosome-associated complex head domain 0.54 38.0 3.47e-01 73.2% 97.8%
1sb7A02 3.30.2340.10 Alpha Beta › 2-Layer Sandwich › Pseudouridine synthase › TruD, insertion domain 0.52 39.0 3.17e-01 80.3% 91.9%
2i53A01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.52 42.0 3.41e-01 91.5% 66.4%
3ejnA03 1.20.120.840 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SusD-like, tetratrico peptide repeats domain 0.51 39.0 3.44e-01 84.5% 96.4%
1qagA01 1.10.418.10 Mainly Alpha › Orthogonal Bundle › Actin-binding Protein, T-fimbrin; domain 1 › Calponin-like domain 0.50 39.0 3.51e-01 90.1% 60.0%
ECOD (40)
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 0.97 93.0 8.19e-01 100.0% 74.2%
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 0.92 79.0 6.78e-01 100.0% 62.1%
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 0.90 78.0 7.19e-01 100.0% 74.7%
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 84.0 7.39e-01 100.0% 72.2%
158313 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 0.82 73.0 6.02e-01 100.0% 67.7%
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 71.0 6.27e-01 100.0% 75.5%
3590072 2004.1.1.70 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › dNK 0.76 59.0 4.10e-01 84.5% 79.6%
4977275 604.1.1.268 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › DUF5658 0.73 53.0 4.59e-01 77.5% 85.5%
3673910 109.4.1.64 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › GET4 0.70 61.0 4.55e-01 100.0% 86.5%
3168466 109.4.1.623 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Cnd1 0.68 59.0 3.55e-01 98.6% 22.3%
3242342 109.49.1.1 ↗ alpha superhelices › Repetitive alpha hairpins › Helical domain in acetyl-CoA carboxylase › Helical domain in acetyl-CoA carboxylase › ACC_central 0.67 55.0 4.30e-01 90.1% 72.3%
3353595 109.4.1.1637 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › U3_assoc_6, UTP6_C 0.67 56.0 3.29e-01 93.0% 16.8%
5001060 1134.1.1.0 ↗ alpha bundles › C-terminal helical domain of alanine-tRNA ligase › C-terminal helical domain of alanine-tRNA ligase › Eukaryotic C-Ala helical domain 0.67 55.0 5.35e-01 93.0% 100.0%
5018946 5079.1.1.1 ↗ alpha duplicates or obligate multimers › Magnesium transporter MgtE membrane domain › Magnesium transporter MgtE membrane domain › Magnesium transporter MgtE membrane domain › MgtE 0.67 47.0 3.53e-01 74.6% 54.6%
4931441 604.39.1.1 ↗ alpha bundles › Spectrin repeat-like › S-component of energy-coupling factor (ECF) transporters › S-component of energy-coupling factor (ECF) transporters › CbiM 0.66 57.0 4.16e-01 98.6% 41.5%
1174232 129.1.1.0 ↗ alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like 0.66 46.0 4.60e-01 73.2% 94.4%
3214955 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.65 54.0 3.35e-01 93.0% 19.8%
3440310 6169.1.1.0 ↗ extended segments › Transmembrane segment of lysosome-associated membrane glycoprotein 2 › Transmembrane segment of lysosome-associated membrane glycoprotein 2 › Transmembrane segment of lysosome-associated membrane glycoprotein 2 0.64 44.0 3.91e-01 71.8% 95.0%
3366795 109.4.1.1637 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › U3_assoc_6, UTP6_C 0.63 51.0 3.12e-01 88.7% 15.5%
3319137 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.63 49.0 4.06e-01 87.3% 51.4%
3428523 185.1.1.5 ↗ alpha superhelices › Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin-like › Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin/Protein HNS-dependent expression A HdeA › Bifunctional inhibitor/lipid-transfer protein/seed storage 2S albumin › Gliadin 0.63 50.0 4.24e-01 88.7% 83.2%
3700350 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.63 49.0 4.14e-01 87.3% 60.8%
3287720 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.62 52.0 3.63e-01 94.4% 30.4%
3656261 109.4.1.957 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_TTI1_N 0.62 50.0 3.83e-01 93.0% 76.7%
5051683 192.5.1.0 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat 0.62 53.0 4.64e-01 98.6% 89.1%
3714155 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.61 45.0 4.06e-01 77.5% 80.0%
3425784 109.4.1.2011 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Cnd1, PF26778 0.61 47.0 3.41e-01 88.7% 39.1%
3581894 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.61 44.0 3.63e-01 78.9% 84.3%
3299098 109.4.1.172 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › MMS19_C 0.61 47.0 3.71e-01 88.7% 44.7%
3708213 109.4.1.494 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Npa1 0.61 51.0 3.41e-01 98.6% 39.1%
3589684 2007.5.1.8 ↗ a/b three-layered sandwiches › Flavodoxin-like › SGNH hydrolase › SGNH hydrolase › Lipase_GDSL_2 0.61 53.0 3.73e-01 97.2% 51.4%
5083232 7531.1.1.1 ↗ a/b three-layered sandwiches › Carbamate kinase-like › Carbamate kinase-like › Carbamate kinase-like › AA_kinase 0.58 48.0 3.16e-01 93.0% 30.3%
3812606 109.4.1.2 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Arm 0.58 45.0 3.32e-01 88.7% 80.0%
3302384 2484.1.1.10 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › TsaD 0.58 51.0 4.02e-01 98.6% 86.0%
3788577 109.4.1.114 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Xpo1,Exportin-T 0.57 48.0 2.96e-01 100.0% 27.6%
5037510 2002.1.1.83 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Amidohydro_1 0.57 49.0 3.66e-01 100.0% 68.4%
4977432 7516.1.1.0 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases 0.56 48.0 3.00e-01 100.0% 23.4%
4551775 3236.1.1.12 ↗ alpha complex topology › Cation-proton antiporter › Cation-proton antiporter (CPA) › Cation-proton antiporter (CPA) › Cons_hypoth698 0.55 45.0 3.02e-01 100.0% 29.3%
3229980 2007.1.9.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › N5-CAIR mutase (phosphoribosylaminoimidazole carboxylase, PurE) 0.54 46.0 3.66e-01 97.2% 87.7%
3929347 7579.1.1.70 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › DUF1057 0.53 45.0 3.00e-01 100.0% 77.5%
D2 medium residues 45-91_157-185_272-283
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00680.26 best RdRP_1 27.0 2.70e-06 69.3% 6.7%
ECOD (5)
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 0.87 82.0 5.22e-01 100.0% 63.5%
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 82.0 5.19e-01 100.0% 63.2%
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 0.85 80.0 5.09e-01 100.0% 61.5%
None — 0.84 78.0 5.02e-01 100.0% 61.5%
4016151 2003.1.3.9 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Nucleotide-binding domain › FMO-like 0.51 33.0 2.28e-01 81.8% 19.7%
D3 medium residues 207-250_301-398
PDB
Domain cluster: rep: RNA_dependent_RNA_polymerase__YP_529897__Newbury_agent_1__331642__D58-79_192-241_281-399
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00680.26 best RdRP_1 35.3 8.00e-09 69.0% 21.8%