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nucleic_acid_binding_protein

Euk-Vir

Grapevine_virus_G

nucleic_acid_binding_protein__YP_009552543__Grapevine_virus_G__2022475

Identity

Accession:
YP_009552543 ↗
Protein ID:
nucleic_acid_binding_protein
Kingdom:
euk

Quality

72.3 mean pLDDT

Taxonomy

Orthornavirae› Kitrinoviricota› Alsuviricetes› Tymovirales› Betaflexiviridae› Vitivirus› Grapevine_virus_G

TaxID: 2022475

Cluster

View cluster (8 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 43-94
PDB
Domain cluster: representative
CATH (29)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2ptfB02 1.20.58.290 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Hypothetical membrane protein ta0354_69_121. 0.74 55.0 5.32e-01 78.8% 93.0%
2qwtA00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.68 56.0 3.97e-01 94.2% 52.7%
3ttvA02 1.20.1370.20 Mainly Alpha › Up-down Bundle › Hemocyanin, N-terminal domain › Catalase, four-helical domain 0.64 44.0 3.51e-01 71.2% 39.4%
4ohcC00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.64 46.0 3.03e-01 76.9% 42.2%
3d1cA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.63 45.0 2.83e-01 75.0% 42.0%
4rk4A02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.61 52.0 3.91e-01 100.0% 79.6%
2ca6A00 3.80.10.10 Alpha Beta › Alpha-Beta Horseshoe › Leucine-rich repeat, LRR (right-handed beta-alpha superhelix) › Ribonuclease Inhibitor 0.61 50.0 3.13e-01 96.2% 15.7%
5yszA03 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.61 51.0 3.86e-01 100.0% 55.4%
1l3lA02 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 0.60 40.0 3.88e-01 71.2% 73.0%
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 0.60 40.0 3.48e-01 71.2% 52.9%
5ufhA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.59 50.0 3.70e-01 100.0% 49.4%
2x0qA04 1.10.510.40 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › 0.59 46.0 3.28e-01 92.3% 88.0%
4xwwA02 3.40.50.10710 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Metallo-hydrolase/oxidoreductase 0.59 49.0 3.65e-01 100.0% 39.3%
3c3kA02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.59 48.0 3.68e-01 98.1% 76.8%
3kjxD01 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.58 41.0 3.91e-01 75.0% 63.9%
3uykA01 3.40.50.2000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Glycogen Phosphorylase B; 0.58 47.0 3.31e-01 98.1% 55.1%
3h5tA03 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.57 46.0 3.47e-01 100.0% 77.7%
3egcD02 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.57 45.0 3.59e-01 98.1% 82.9%
6uglB02 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 0.56 39.0 3.86e-01 75.0% 77.6%
5a0tB01 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.56 45.0 2.86e-01 94.2% 16.7%
6v7xB02 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 37.0 3.70e-01 71.2% 85.7%
3t5qG01 1.10.150.550 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Arenavirus nucleocapsid protein, head domain 0.53 37.0 3.16e-01 80.8% 91.3%
7r3bE01 3.30.300.10 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › 0.53 39.0 3.44e-01 82.7% 84.1%
4chgA00 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.53 41.0 3.28e-01 98.1% 51.1%
1m0sA01 3.40.50.1360 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.52 43.0 3.26e-01 98.1% 67.8%
3nrhA00 1.20.120.1550 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Protein of unknown function DUF5063 0.52 39.0 2.95e-01 88.5% 90.5%
1q48A00 3.90.1010.10 Alpha Beta › Alpha-Beta Complex › Sufe protein. Chain: A › 0.52 36.0 2.80e-01 75.0% 41.0%
4rflA01 3.40.50.1970 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.52 43.0 3.29e-01 98.1% 51.1%
2aeeB00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.51 43.0 3.00e-01 100.0% 61.1%
ECOD (12)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4455495 176.1.1.1 ↗ alpha arrays › Annexin › Annexin › Annexin › Annexin 0.62 51.0 4.59e-01 96.2% 100.0%
3600551 10.12.1.0 ↗ beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix 0.61 48.0 2.99e-01 88.5% 58.2%
3975610 101.1.3.1 ↗ alpha arrays › HTH › HTH › tetra-helical, LuxR-like › GerE 0.60 41.0 3.76e-01 71.2% 65.7%
2761 101.1.3.1 ↗ alpha arrays › HTH › HTH › tetra-helical, LuxR-like › GerE 0.60 40.0 3.48e-01 71.2% 52.9%
5072206 182.1.3.3 ↗ alpha complex topology › Cryptochrome/photolyase FAD-binding domain-related › Cryptochrome/photolyase FAD-binding domain-related › PriX › DNA_primase_lrg 0.59 44.0 3.48e-01 84.6% 44.2%
3969657 101.1.3.1 ↗ alpha arrays › HTH › HTH › tetra-helical, LuxR-like › GerE 0.59 39.0 3.60e-01 71.2% 61.3%
3289143 101.1.3.1 ↗ alpha arrays › HTH › HTH › tetra-helical, LuxR-like › GerE 0.58 40.0 3.50e-01 73.1% 55.3%
4404485 101.1.3.1 ↗ alpha arrays › HTH › HTH › tetra-helical, LuxR-like › GerE 0.56 38.0 3.70e-01 71.2% 76.7%
3241675 145.1.1.0 ↗ alpha arrays › F-box domain › F-box domain › F-box domain 0.56 41.0 4.12e-01 84.6% 94.5%
4962870 101.1.2.101 ↗ alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.54 43.0 3.45e-01 98.1% 98.4%
4093975 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.51 42.0 3.35e-01 98.1% 73.3%
3367636 7575.1.1.11 ↗ a/b three-layered sandwiches › Caspase-like › Caspase-like › Caspase-like › PF31181 0.51 41.0 2.67e-01 100.0% 31.4%