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YP_009218472.1

Arc-Vir

NC_029011__YP_009218472.1__AVT99-gp08__00008

Identity

Accession:
NC_029011 ↗
Protein ID:
YP_009218472.1 ↗
Kingdom:
archaea

Quality

94.8 mean pLDDT

Taxonomy

Bicaudaviridae› Sulfolobus_monocaudavirus_SMV4

TaxID: 1732178

Cluster

Singleton — not in a non-trivial cluster

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 195-252
PDB
Domain cluster: representative
CATH (52)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3qo8A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.88 70.0 5.67e-01 86.2% 50.9%
7ymiZ01 1.10.287.740 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre 0.87 67.0 6.76e-01 82.8% 89.7%
1lrzA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.86 67.0 6.59e-01 82.8% 80.6%
3k6tB00 1.20.5.4010 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.85 58.0 6.24e-01 94.8% 83.7%
1vf7A03 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.84 67.0 6.71e-01 86.2% 83.3%
4l8jA04 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.84 67.0 6.75e-01 86.2% 84.7%
3fd9A03 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.84 67.0 6.17e-01 86.2% 69.9%
2kw6A00 6.10.140.1300 Special › Helix non-globular › Helix Hairpins › 0.83 57.0 5.47e-01 70.7% 70.8%
1i4dA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.82 65.0 4.48e-01 86.2% 27.1%
2pvqA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.81 56.0 4.55e-01 84.5% 39.6%
2rp4A00 6.10.280.60 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Transcription factor p53, C-terminal domain 0.81 66.0 6.15e-01 100.0% 71.8%
4iggA01 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.80 62.0 5.98e-01 84.5% 79.1%
2itbB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.79 69.0 4.68e-01 96.6% 32.3%
4abxA02 6.10.140.1090 Special › Helix non-globular › Helix Hairpins › 0.78 62.0 5.42e-01 86.2% 62.1%
3gnlB02 1.10.287.1890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.78 59.0 5.63e-01 82.8% 70.6%
3vnxA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.78 70.0 4.77e-01 100.0% 64.1%
3ismC01 1.25.40.240 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Ku, C-terminal domain 0.78 69.0 5.06e-01 100.0% 50.0%
7ymiD01 1.20.85.10 Mainly Alpha › Up-down Bundle › Photosynthetic Reaction Center, subunit M; domain 1 › Photosystem II protein D1-like 0.77 68.0 4.80e-01 100.0% 63.9%
1qu7A00 1.10.287.950 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Methyl-accepting chemotaxis protein 0.77 60.0 4.03e-01 87.9% 24.7%
8alzB08 1.10.3380.10 Mainly Alpha › Orthogonal Bundle › Sec63 N-terminal domain-like fold › Sec63 N-terminal domain-like domain 0.76 70.0 5.26e-01 100.0% 79.4%
2cazD00 6.10.140.820 Special › Helix non-globular › Helix Hairpins › 0.76 57.0 5.71e-01 81.0% 80.0%
4dyqA01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.76 66.0 5.54e-01 100.0% 76.7%
2e9xA01 1.20.58.1030 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.76 69.0 5.24e-01 100.0% 57.0%
4abyD00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.74 59.0 3.65e-01 86.2% 20.3%
3bt5A00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.74 63.0 4.75e-01 100.0% 82.1%
1lkoA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.73 63.0 4.82e-01 100.0% 78.6%
2js5A00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.73 56.0 5.29e-01 86.2% 74.6%
2o8pA00 1.20.190.20 Mainly Alpha › Up-down Bundle › Delta-Endotoxin; domain 1 › 14-3-3 domain 0.72 62.0 4.23e-01 100.0% 39.3%
1x4tA01 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.71 53.0 5.35e-01 84.5% 82.8%
1zpyA00 6.10.140.1960 Special › Helix non-globular › Helix Hairpins › 0.71 62.0 5.37e-01 98.3% 69.2%
6xxvC00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.70 60.0 4.90e-01 96.6% 75.7%
2yqyA00 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.70 58.0 4.46e-01 89.7% 65.9%
3fxdB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 55.0 5.52e-01 89.7% 86.2%
3tklB01 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 54.0 5.30e-01 86.2% 80.6%
2l35A00 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.70 53.0 5.20e-01 84.5% 79.4%
3q15B00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.68 60.0 3.73e-01 100.0% 23.5%
2jdiG01 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.68 49.0 4.85e-01 94.8% 73.8%
2v0xA01 1.10.287.3160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.68 58.0 4.25e-01 98.3% 59.5%
4asvA00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.68 46.0 4.23e-01 72.4% 57.0%
1yxrA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.67 56.0 5.29e-01 100.0% 77.0%
3l9fA02 6.10.140.1570 Special › Helix non-globular › Helix Hairpins › 0.67 58.0 5.26e-01 100.0% 93.8%
3sfvB02 6.10.140.2010 Special › Helix non-globular › Helix Hairpins › 0.67 50.0 3.56e-01 86.2% 25.5%
4oe8C00 1.10.8.1170 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.65 54.0 4.69e-01 94.8% 60.9%
8igrI01 2.40.270.10 Mainly Beta › Beta Barrel › Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 › DNA-directed RNA polymerase, subunit 2, domain 6 0.65 53.0 3.75e-01 89.7% 83.5%
3mq1A01 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.65 54.0 4.76e-01 100.0% 85.9%
3bvoA02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.64 57.0 4.97e-01 96.6% 73.3%
3dcfA02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.64 51.0 3.89e-01 89.7% 42.3%
2v6eA01 1.10.287.3180 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.64 50.0 4.66e-01 86.2% 89.3%
3qf7A02 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.63 47.0 4.65e-01 84.5% 79.4%
3h36A00 1.10.10.400 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Polyribonucleotide nucleotidyltransferase, RNA-binding domain 0.61 50.0 4.58e-01 91.4% 67.9%
2d9dA00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.60 50.0 4.47e-01 100.0% 67.4%
2xvtC00 1.10.150.510 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Receptor activity modifying family 0.54 45.0 4.17e-01 100.0% 77.2%
ECOD (34)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4010384 361.1.1.0 ↗ few secondary structure elements › DnaJ/Hsp40 cysteine-rich domain › DnaJ/Hsp40 cysteine-rich domain › DnaJ/Hsp40 cysteine-rich domain 0.90 72.0 6.90e-01 84.5% 83.1%
3172138 3846.1.1.0 ↗ alpha bundles › IcmR › IcmR › IcmR 0.90 68.0 6.52e-01 82.8% 70.8%
4974737 2003.1.5.66 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_11 0.90 68.0 4.28e-01 82.8% 18.1%
3979099 361.1.1.0 ↗ few secondary structure elements › DnaJ/Hsp40 cysteine-rich domain › DnaJ/Hsp40 cysteine-rich domain › DnaJ/Hsp40 cysteine-rich domain 0.89 72.0 5.15e-01 86.2% 35.5%
4171766 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.89 72.0 6.11e-01 86.2% 55.6%
3862656 3939.1.1.182 ↗ alpha duplicates or obligate multimers › XRCC4 C-terminal oligomerization domain › XRCC4 C-terminal oligomerization domain › XRCC4 C-terminal oligomerization domain › KIF21A_2nd 0.89 73.0 4.94e-01 87.9% 30.5%
5057918 7516.1.1.2 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glycos_transf_2 0.88 69.0 4.20e-01 82.8% 43.1%
3623143 192.4.1.0 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) 0.88 71.0 6.17e-01 86.2% 67.1%
3600217 5054.1.1.0 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels 0.87 80.0 5.11e-01 100.0% 29.6%
3218199 192.4.1.0 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) 0.87 70.0 5.95e-01 86.2% 63.3%
4601944 3922.1.1.0 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 0.85 68.0 6.25e-01 86.2% 66.7%
4077176 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.85 68.0 5.80e-01 86.2% 55.6%
3276221 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.84 65.0 4.92e-01 82.8% 42.3%
4937014 2004.1.1.87 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N 0.84 66.0 3.93e-01 84.5% 13.2%
3969893 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.83 66.0 6.36e-01 86.2% 76.9%
4034416 2004.1.1.481 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N, AAA_29 0.83 69.0 4.09e-01 89.7% 26.4%
3987794 1075.1.2.16 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain › DUF1430 0.83 66.0 4.05e-01 86.2% 15.5%
3713097 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.83 71.0 4.32e-01 93.1% 76.1%
3964934 2004.1.1.87 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N 0.82 65.0 3.70e-01 86.2% 9.6%
3590383 5082.1.1.1 ↗ alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation_efflux 0.81 73.0 4.96e-01 100.0% 70.5%
3991544 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.81 66.0 5.44e-01 87.9% 71.0%
3788505 3755.3.1.126 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › PEX11 0.80 70.0 5.22e-01 98.3% 66.2%
3239952 2004.1.1.442 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N, AAA_21 0.77 71.0 4.13e-01 100.0% 58.9%
3718969 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.77 59.0 4.22e-01 84.5% 28.0%
None — 0.77 68.0 4.52e-01 100.0% 28.6%
4438700 622.1.1.0 ↗ alpha bundles › YvfG-like › HSC20 (HSCB), C-terminal oligomerisation domain › HSC20 (HSCB), C-terminal oligomerisation domain 0.75 67.0 5.88e-01 100.0% 75.3%
5075524 2484.1.1.302 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Cas12f1-like_TNB 0.74 58.0 3.99e-01 84.5% 45.6%
3718156 101.1.9.0 ↗ alpha arrays › HTH › HTH › Putative DNA-binding domain 0.72 65.0 5.49e-01 100.0% 75.8%
3230196 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.70 62.0 4.90e-01 100.0% 62.5%
4943621 150.1.1.204 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › VIT1 0.69 58.0 4.60e-01 100.0% 81.5%
3249849 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.68 58.0 4.81e-01 100.0% 73.6%
3617829 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.68 59.0 4.65e-01 100.0% 77.6%
3714244 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.66 52.0 5.17e-01 91.4% 90.0%
3565062 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.62 51.0 4.02e-01 100.0% 78.6%
D2 medium residues 1-75
PDB
Domain cluster: rep: IMGVR_UViG_3300027932_000064-3300027932-Ga0208429_1000321__D4-72