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nucleic_acid-binding_protein

Euk-Vir

Caucasus_prunus_virus

nucleic_acid-binding_protein__YP_009505635__Caucasus_prunus_virus__1667230

Identity

Accession:
YP_009505635 ↗
Protein ID:
nucleic_acid-binding_protein
Kingdom:
euk

Quality

66.1 mean pLDDT

Taxonomy

Orthornavirae› Kitrinoviricota› Alsuviricetes› Tymovirales› Betaflexiviridae› Prunevirus› Caucasus_prunus_virus

TaxID: 1667230

Cluster

View cluster (2 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 medium residues 1-51
PDB
Domain cluster: representative
CATH (39)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2a3vB01 1.10.150.130 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain 0.83 61.0 4.92e-01 78.4% 42.6%
6lumD01 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.79 61.0 4.61e-01 86.3% 83.2%
2fcwA00 1.20.81.10 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › RAP domain 0.75 63.0 4.97e-01 94.1% 48.1%
2g7zA01 3.40.50.10170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.75 51.0 3.65e-01 72.5% 40.6%
3lupA01 3.40.50.10170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.75 53.0 3.76e-01 76.5% 59.4%
5l3wA01 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.74 55.0 4.69e-01 84.3% 48.8%
3nctA00 3.40.50.11880 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Plasmid SOS inhibition protein 0.73 52.0 3.83e-01 76.5% 45.3%
1tj7A03 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.73 51.0 4.61e-01 76.5% 53.5%
2x9qB00 3.40.50.11710 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Cyclodipeptide synthase 0.72 55.0 3.63e-01 84.3% 19.4%
1dmhA00 2.60.130.10 Mainly Beta › Sandwich › Protocatechuate 3,4-Dioxygenase, subunit A › Aromatic compound dioxygenase 0.71 54.0 3.32e-01 82.4% 14.2%
1tfeA02 1.10.286.20 Mainly Alpha › Orthogonal Bundle › GTP Cyclohydrolase I; Chain A, domain 1 › 0.70 50.0 5.24e-01 78.4% 91.1%
2gtsA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.70 52.0 4.55e-01 80.4% 79.2%
3l9wA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.70 60.0 4.22e-01 98.0% 88.3%
2lqxA00 6.10.250.1700 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.70 50.0 5.37e-01 82.4% 97.6%
5axmB00 3.30.70.3000 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › tRNA(His) guanylyltransferase (Thg1) 0.69 59.0 3.78e-01 94.1% 45.2%
4m70B00 1.10.246.200 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › WPP domain 0.68 56.0 4.71e-01 94.1% 61.5%
4h8aB01 1.10.1530.10 Mainly Alpha › Orthogonal Bundle › Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 › Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel 0.67 48.0 4.63e-01 76.5% 65.0%
1cf7B00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.67 53.0 4.56e-01 88.2% 56.1%
3cqyB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.67 54.0 3.74e-01 92.2% 41.3%
4rg8A04 1.10.287.1240 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.66 45.0 4.17e-01 72.5% 58.1%
1yqgA02 1.10.3730.10 Mainly Alpha › Orthogonal Bundle › ProC C-terminal domain-like fold › ProC C-terminal domain-like 0.66 55.0 4.30e-01 94.1% 42.5%
3u9jA00 1.20.120.520 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › nmb1532 protein domain like 0.66 53.0 3.87e-01 94.1% 70.7%
3l6gA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.66 47.0 3.49e-01 80.4% 32.0%
4xrpA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.66 53.0 3.87e-01 90.2% 47.5%
3bvoA02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.65 51.0 4.26e-01 84.3% 51.2%
3cjlA00 3.10.20.850 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Protein of unknown function DUF3861 0.65 53.0 4.53e-01 94.1% 58.0%
3clmA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.65 55.0 3.38e-01 100.0% 54.8%
2yevA02 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.62 47.0 4.23e-01 84.3% 64.9%
3c3dA02 1.10.8.240 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › CofD-like domain 0.60 41.0 3.57e-01 74.5% 69.3%
1p4wA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.59 42.0 3.54e-01 74.5% 71.3%
3bhgA01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.57 38.0 3.06e-01 84.3% 32.2%
2ftxA00 3.30.457.50 Alpha Beta › 2-Layer Sandwich › Copper Amine Oxidase; Chain A, domain 1 › Chromosome segregation protein Spc25 0.57 44.0 3.77e-01 88.2% 79.8%
4azcA02 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.57 42.0 4.03e-01 80.4% 86.4%
3nynA03 1.10.167.10 Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › Regulator of G-protein Signalling 4, domain 2 0.56 38.0 3.35e-01 72.5% 45.7%
5xsoA02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.55 38.0 3.34e-01 72.5% 52.6%
2vsyA03 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.55 46.0 3.16e-01 94.1% 73.2%
2i7uA00 6.10.250.1010 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.54 39.0 3.78e-01 84.3% 91.9%
1ze0A01 1.20.120.700 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › nitrate reductase, subunit delta (NarJ) 0.53 40.0 3.52e-01 88.2% 88.1%
4r16A02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 41.0 2.80e-01 92.2% 37.6%
ECOD (30)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3689259 5076.1.1.1 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Mitochondrial ADP/ATP carrier › Mitochondrial ADP/ATP carrier › Mito_carr 0.90 83.0 4.96e-01 100.0% 54.0%
3491670 614.1.1.0 ↗ alpha duplicates or obligate multimers › L27 domain › L27 domain › L27 domain 0.88 69.0 6.78e-01 84.3% 78.2%
3723375 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.85 73.0 4.52e-01 94.1% 29.9%
3213226 3075.1.1.0 ↗ a+b two layers › ubiquitin-binding domain from PLAA › ubiquitin-binding domain from PLAA › ubiquitin-binding domain from PLAA 0.84 65.0 5.96e-01 82.4% 67.7%
5031036 3979.1.1.0 ↗ a+b four layers › Mre11 nuclease C-terminal domain › Mre11 nuclease C-terminal domain › Mre11 nuclease C-terminal domain 0.84 63.0 4.84e-01 80.4% 61.8%
3621479 6026.1.1.1 ↗ alpha duplicates or obligate multimers › cwf21 domain › cwf21 domain › cwf21 domain › cwf21 0.84 68.0 5.61e-01 86.3% 55.3%
4945127 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.84 62.0 5.13e-01 78.4% 60.0%
4597483 5058.1.1.1 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › MS_channel_1st_1,MS_channel_1st 0.83 68.0 5.11e-01 90.2% 40.8%
2647290 225.1.1.6 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c_2 0.80 63.0 5.44e-01 88.2% 57.5%
3344802 6158.1.1.0 ↗ alpha bundles › Nucleoporin p58/p45 helical region › Nucleoporin p58/p45 helical region › Nucleoporin p58/p45 helical region 0.78 65.0 5.99e-01 90.2% 76.9%
3232753 632.2.1.21 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains › ANIS5_cation-bd 0.77 55.0 4.89e-01 74.5% 61.4%
3744658 206.1.1.14 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › ABC1 0.76 59.0 3.38e-01 84.3% 8.8%
3220288 509.1.1.14 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › ANIS5_cation-bd 0.75 51.0 4.72e-01 70.6% 63.1%
3518592 102.1.2.28 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › DNA-glycosylase › PF26091 0.74 66.0 5.42e-01 100.0% 55.6%
4988048 3788.1.1.0 ↗ alpha bundles › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) 0.74 59.0 5.65e-01 88.2% 83.3%
3909017 192.5.1.1 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1 0.74 56.0 4.57e-01 80.4% 52.2%
4018370 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.74 55.0 4.06e-01 80.4% 50.8%
3236352 4177.1.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.70 59.0 4.04e-01 94.1% 85.9%
3500138 564.1.1.0 ↗ alpha arrays › N-terminal, cytoplasmic domain of anti-sigma factors › N-terminal, cytoplasmic domain of anti-sigma factors › N-terminal, cytoplasmic domain of anti-sigma factors 0.70 50.0 4.72e-01 74.5% 65.0%
4197827 230.3.1.1 ↗ a+b two layers › T-fold › Elongation factor Ts (EF-Ts), dimerisation domain › Elongation factor Ts (EF-Ts), dimerisation domain › EF_TS 0.70 59.0 4.26e-01 94.1% 56.6%
4243432 2004.1.1.499 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DEAD_2, Helicase_C_2 0.69 56.0 3.21e-01 92.2% 9.4%
3823984 284.1.3.0 ↗ a+b two layers › FKBP-like › FKBP-like › WNK1 autoinhibitory domain 0.69 52.0 4.29e-01 92.2% 44.0%
4388170 103.1.1.6 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain › RuvA_C 0.69 47.0 4.52e-01 72.5% 61.7%
3669542 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.68 51.0 3.43e-01 84.3% 21.0%
4952257 3567.1.1.0 ↗ a+b duplicates or obligate multimers › MPER trimer › MPER trimer › MPER trimer 0.66 50.0 4.06e-01 84.3% 43.3%
4107264 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.66 56.0 4.43e-01 100.0% 61.7%
3304689 109.4.1.189 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR_2 0.66 44.0 3.08e-01 70.6% 41.2%
4028555 4099.1.1.0 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.65 46.0 4.16e-01 76.5% 74.7%
3985609 304.55.1.8 ↗ a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › TrwC 0.57 45.0 3.29e-01 92.2% 91.9%
4623707 821.1.1.1 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG 0.56 37.0 3.08e-01 70.6% 62.1%