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YP_010581811.1

Arc-Vir

NC_003158__YP_010581811.1__CWS96-gp21__00021

Identity

Accession:
NC_003158 ↗
Protein ID:
YP_010581811.1 ↗
Kingdom:
archaea

Quality

90.9 mean pLDDT

Taxonomy

Helvetiavirae› Dividoviricota› Laserviricetes› Halopanivirales› Simuloviridae› Yingchengvirus› Saline_Natrinema_sp._J7-1_virus_1

TaxID: 2847285

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 medium residues 1-78
PDB
Domain cluster: representative
CATH (25)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3a98B01 6.10.10.90 Special › Helix non-globular › Helicase, Ruva Protein; domain 3 › 0.69 48.0 4.80e-01 80.8% 69.1%
1cxzB00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.68 51.0 4.95e-01 78.2% 73.3%
4hr1A00 1.20.1270.410 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.66 47.0 4.05e-01 73.1% 67.8%
3uo2B02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.65 49.0 4.77e-01 78.2% 78.6%
6r1nA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.65 47.0 4.25e-01 75.6% 57.3%
3rrkA02 1.20.1460.20 Mainly Alpha › Up-down Bundle › subunit c (vma5p) of the yeast v-atpase, domain 2 › 0.63 48.0 3.89e-01 83.3% 72.3%
2j0nB00 1.20.1710.10 Mainly Alpha › Up-down Bundle › IpaD-like › IpaD-like 0.63 46.0 3.44e-01 76.9% 41.2%
4dloB02 1.25.40.610 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.62 37.0 3.23e-01 96.2% 38.5%
4fwvA02 1.20.120.1680 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.62 55.0 4.61e-01 100.0% 96.3%
1qgtB00 1.10.4090.10 Mainly Alpha › Orthogonal Bundle › Hepatitis B viral capsid (hbcag) fold › Viral capsid, core domain supefamily, Hepatitis B virus 0.61 43.0 3.56e-01 74.4% 66.4%
2d4uB00 1.20.120.30 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Aspartate receptor, ligand-binding domain 0.60 46.0 3.78e-01 85.9% 46.5%
4mndA02 1.20.120.1760 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CDP-alcohol phosphotransferase transmembrane (TM) domain 0.60 44.0 3.30e-01 78.2% 32.5%
2d9dA00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.59 38.0 3.72e-01 75.6% 57.3%
1hciA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.59 44.0 3.83e-01 80.8% 53.2%
4aifA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.59 38.0 3.09e-01 73.1% 34.7%
2ipcA04 1.10.3060.10 Mainly Alpha › Orthogonal Bundle › Helical scaffold and wing domains of SecA › Helical scaffold and wing domains of SecA 0.58 48.0 3.46e-01 93.6% 31.4%
6cnzF00 1.20.59.10 Mainly Alpha › Up-down Bundle › Chorismate Mutase Domain, subunit A › Chorismate mutase 0.58 43.0 3.45e-01 79.5% 39.9%
1wa8A00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.58 46.0 4.31e-01 88.5% 72.7%
6t4hA03 1.10.3060.10 Mainly Alpha › Orthogonal Bundle › Helical scaffold and wing domains of SecA › Helical scaffold and wing domains of SecA 0.57 48.0 3.78e-01 94.9% 44.2%
4b1bA00 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.57 45.0 2.92e-01 91.0% 17.8%
1m6nA04 1.10.3060.10 Mainly Alpha › Orthogonal Bundle › Helical scaffold and wing domains of SecA › Helical scaffold and wing domains of SecA 0.56 44.0 3.75e-01 87.2% 51.9%
5k29A00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.56 40.0 3.73e-01 75.6% 96.9%
1i6zA00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.55 43.0 3.67e-01 87.2% 51.1%
1cm5A00 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.55 45.0 2.61e-01 92.3% 14.4%
2dk4A00 4.10.280.110 Few Secondary Structures › Irregular › MYOD Basic-Helix-Loop-Helix Domain, subunit B › Pre-mRNA processing factor 4 domain 0.52 35.0 3.61e-01 83.3% 72.4%
ECOD (28)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4020083 7015.1.1.0 ↗ alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain 0.74 51.0 4.17e-01 71.8% 42.9%
5020645 7516.1.1.2 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glycos_transf_2 0.71 55.0 3.72e-01 83.3% 24.8%
3864955 633.22.1.6 ↗ alpha bundles › Bromodomain-like › Vitamin K epoxide reductase (VKOR) › Vitamin K epoxide reductase (VKOR) › TMD0_ABC 0.70 49.0 3.78e-01 73.1% 75.3%
2325657 601.4.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.70 50.0 4.07e-01 75.6% 42.3%
3204414 1.1.17.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 2 0.68 53.0 3.32e-01 82.1% 65.4%
3783410 192.15.1.2 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › Mod_r 0.66 52.0 4.48e-01 83.3% 60.0%
3445025 174.1.1.2 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Jagunal 0.66 54.0 4.33e-01 89.7% 90.3%
4323650 2004.1.1.45 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MutS_V 0.65 52.0 3.37e-01 100.0% 21.3%
3481568 3998.1.1.1 ↗ alpha arrays › Peptidase inhibitors family I29 › Peptidase inhibitors family I29 › Peptidase inhibitors family I29 › Inhibitor_I29 0.65 43.0 4.58e-01 79.5% 77.1%
4016004 5069.1.1.0 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes 0.63 49.0 3.74e-01 84.6% 73.3%
3598050 192.4.1.0 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) 0.62 40.0 4.00e-01 98.7% 63.7%
3555461 150.1.1.100 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › TMD0_ABC 0.62 46.0 3.43e-01 80.8% 64.4%
4651060 633.22.1.0 ↗ alpha bundles › Bromodomain-like › Vitamin K epoxide reductase (VKOR) › Vitamin K epoxide reductase (VKOR) 0.61 45.0 3.54e-01 78.2% 77.0%
3427223 633.4.1.1 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.61 49.0 3.95e-01 89.7% 93.5%
3611632 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.59 43.0 3.99e-01 76.9% 82.0%
3221299 310.2.1.0 ↗ a+b two layers › RRF/tRNA synthetase additional domain-like › Ribosome recycling factor, RRF › Ribosome recycling factor, RRF 0.58 44.0 3.70e-01 84.6% 46.7%
3476125 109.4.1.373 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › COG4_m 0.58 51.0 3.75e-01 98.7% 74.9%
3665032 2003.1.2.8 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_2,Pyr_redox_2 0.58 50.0 3.67e-01 100.0% 45.1%
3219804 371.1.1.0 ↗ few secondary structure elements › Phospholipase A2, PLA2 › Phospholipase A2, PLA2 › Phospholipase A2, PLA2 0.57 36.0 3.30e-01 100.0% 47.6%
3516873 159.1.1.3 ↗ alpha bundles › all-alpha NTP pyrophosphatases › all-alpha NTP pyrophosphatases › Hypothetical protein AF_0060 › DUF1599 0.56 36.0 3.65e-01 73.1% 63.7%
3960011 150.8.1.2 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › PPE › PPE › EspB_PPE 0.56 48.0 3.91e-01 100.0% 94.4%
3404270 377.1.1.0 ↗ few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.56 51.0 4.27e-01 100.0% 70.8%
3281424 3755.3.1.299 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › DUF445 0.55 45.0 3.63e-01 94.9% 49.4%
4879470 5057.1.1.1 ↗ alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neur_chan_memb 0.55 39.0 4.02e-01 75.6% 81.3%
3638504 2492.1.1.4 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like 0.54 48.0 3.09e-01 98.7% 31.0%
5057229 371.1.1.0 ↗ few secondary structure elements › Phospholipase A2, PLA2 › Phospholipase A2, PLA2 › Phospholipase A2, PLA2 0.54 45.0 3.93e-01 97.4% 59.2%
3939588 5057.1.1.1 ↗ alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neur_chan_memb 0.54 49.0 3.92e-01 100.0% 53.3%
3720672 109.4.1.1591 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › U-box 0.52 43.0 3.09e-01 98.7% 27.1%
D2 medium residues 79-154
PDB
Domain cluster: representative
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3ilkA02 1.10.8.590 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.69 42.0 4.47e-01 98.7% 69.1%
2ii2A02 1.10.220.10 Mainly Alpha › Orthogonal Bundle › Annexin V; domain 1 › Annexin 0.66 41.0 4.61e-01 75.0% 82.8%
4flbA00 1.25.40.90 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.59 41.0 3.50e-01 81.6% 42.7%
3d3oA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.59 37.0 2.91e-01 78.9% 27.3%
2o35A00 1.10.3340.10 Mainly Alpha › Orthogonal Bundle › SMc04008-like fold › SMc04008-like 0.59 42.0 4.17e-01 75.0% 79.7%
3er9B01 1.20.1270.320 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Poxvirus poly(A) polymerase, N domain 0.54 41.0 3.75e-01 82.9% 69.8%
1bccA02 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.53 41.0 3.06e-01 85.5% 76.5%
2zj2A04 1.10.3380.20 Mainly Alpha › Orthogonal Bundle › Sec63 N-terminal domain-like fold › 0.52 41.0 3.27e-01 88.2% 64.1%
1cg2A01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.52 44.0 2.97e-01 92.1% 62.7%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5064030 182.1.3.0 ↗ alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › PriX 0.62 38.0 3.56e-01 77.6% 49.5%
1654945 4048.1.1.1 ↗ alpha bundles › Second alpha-helical domain in heme-dependent catalases › Second alpha-helical domain in heme-dependent catalases › Second alpha-helical domain in heme-dependent catalases › Catalase-rel 0.56 44.0 4.19e-01 85.5% 83.5%
3937548 109.27.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › BACK domain › BACK domain 0.55 38.0 3.03e-01 71.1% 64.0%
3579629 309.1.1.0 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › LuxS/MPP-like metallohydrolase 0.54 41.0 3.15e-01 81.6% 56.0%
3881657 170.1.1.0 ↗ alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C 0.53 39.0 3.90e-01 80.3% 87.5%
3569301 309.1.1.4 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › LuxS/MPP-like metallohydrolase › Peptidase_M16_C 0.53 42.0 2.99e-01 86.8% 65.3%
4987010 2006.1.4.2 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › PIN 0.52 39.0 3.23e-01 77.6% 76.6%
3801667 2498.1.1.0 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" 0.51 43.0 3.14e-01 96.1% 51.3%
3519399 170.1.1.0 ↗ alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein-C › Retrovirus capsid protein-C 0.51 36.0 3.47e-01 76.3% 77.8%