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nucleic_acid_binding_protein

Euk-Vir

Ligustrum_virus_A

nucleic_acid_binding_protein__YP_009288961__Ligustrum_virus_A__1899566

Identity

Accession:
YP_009288961 ↗
Protein ID:
nucleic_acid_binding_protein
Kingdom:
euk

Quality

73.7 mean pLDDT

Taxonomy

Orthornavirae› Kitrinoviricota› Alsuviricetes› Tymovirales› Betaflexiviridae› Carlavirus› Ligustrum_virus_A

TaxID: 1899566

Cluster

View cluster (30 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 3-36
PDB
Domain cluster: representative
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1sxjA02 1.10.8.60 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.89 74.0 5.86e-01 97.1% 45.8%
1knzA01 6.10.280.20 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Rotavirus non-structural protein NSP3, N-terminal domain 0.82 69.0 4.97e-01 100.0% 33.3%
6pd2A01 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.81 65.0 3.92e-01 100.0% 13.6%
1w8iA00 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.80 65.0 4.25e-01 100.0% 21.4%
3fynA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.80 64.0 4.26e-01 100.0% 22.4%
3d0wA00 1.10.760.20 Mainly Alpha › Orthogonal Bundle › Cytochrome Bc1 Complex; Chain D, domain 2 › Protein of unknown function DUF3243 0.80 63.0 4.90e-01 100.0% 40.7%
2bsqA00 3.40.50.1010 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 5'-nuclease 0.79 65.0 4.35e-01 100.0% 24.5%
3u9rB02 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.77 61.0 3.64e-01 100.0% 12.2%
2h92A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.77 62.0 3.85e-01 100.0% 15.7%
1wgfA01 1.10.30.10 Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › High mobility group box domain 0.75 59.0 5.37e-01 100.0% 71.7%
3zfvA02 3.30.70.1900 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.75 63.0 4.10e-01 100.0% 47.4%
4ixjA01 3.30.1300.80 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › 0.75 63.0 4.91e-01 100.0% 49.4%
1v64A00 1.10.30.10 Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › High mobility group box domain 0.73 59.0 4.26e-01 100.0% 31.5%
3ermB00 1.10.10.710 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › PSPTO_1197 like 0.73 57.0 4.94e-01 100.0% 59.4%
3bh0A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.73 62.0 3.65e-01 100.0% 65.1%
4g9pA01 3.20.20.20 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Dihydropteroate synthase-like 0.71 56.0 3.35e-01 100.0% 23.0%
3pfyA02 6.10.20.180 Special › Helix non-globular › Arc Repressor Mutant, subunit A › 0.71 59.0 5.11e-01 97.1% 64.9%
4v19K02 1.10.10.250 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Ribosomal protein L11/L12, C-terminal domain 0.68 53.0 4.34e-01 97.1% 73.3%
1ks9A02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.65 50.0 3.62e-01 97.1% 27.6%
2j5iA02 6.10.250.2850 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.64 48.0 4.76e-01 91.2% 97.4%
3d3oA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.63 49.0 3.24e-01 97.1% 18.8%
1jq5A02 1.20.1090.10 Mainly Alpha › Up-down Bundle › Dehydroquinate synthase-like, alpha domain › Dehydroquinate synthase-like - alpha domain 0.61 47.0 3.01e-01 100.0% 51.9%
4i8oA03 1.10.8.1130 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Bacterial toxin RNase RnlA/LsoA, C-terminal Dmd-binding domain 0.59 45.0 3.93e-01 100.0% 52.2%
6jrpA01 1.10.30.10 Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › High mobility group box domain 0.57 39.0 3.66e-01 100.0% 54.1%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5066354 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.91 76.0 6.54e-01 97.1% 60.0%
3885028 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.90 79.0 5.82e-01 100.0% 40.0%
3643488 192.15.1.11 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › CemA 0.86 73.0 5.70e-01 100.0% 45.3%
2776079 3787.1.1.0 ↗ alpha bundles › HAD superfamily helical bundle insertion domain 0.86 72.0 6.20e-01 100.0% 59.6%
4038157 103.5.1.0 ↗ alpha arrays › RuvA-C › post-HMGL domain-like › post-HMGL domain-like 0.82 66.0 5.88e-01 91.2% 68.0%
3784931 2484.1.1.2 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Actin 0.78 64.0 3.78e-01 100.0% 69.6%
3737764 130.1.1.1 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif › SAP 0.77 60.0 4.94e-01 100.0% 70.7%
3458313 145.1.1.0 ↗ alpha arrays › F-box domain › F-box domain › F-box domain 0.77 63.0 6.38e-01 100.0% 100.0%
3231907 2006.1.4.39 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like › C_tripleX 0.76 62.0 5.84e-01 100.0% 86.7%
3220837 397.7.1.0 ↗ few secondary structure elements › Toxic hairpin › Ribosome-inactivating protein luffin P1 › Ribosome-inactivating protein luffin P1 0.76 63.0 6.10e-01 100.0% 97.5%
4263826 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.76 62.0 5.06e-01 100.0% 48.6%
3722621 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.74 59.0 4.90e-01 100.0% 47.1%
7661 4188.1.1.1 ↗ a+b complex topology › BB1717-like › BB1717-like › BB1717-like › SRAP 0.73 59.0 3.63e-01 100.0% 43.6%
3715403 190.1.1.0 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box 0.69 53.0 4.75e-01 100.0% 58.3%
3743890 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.66 51.0 3.53e-01 100.0% 75.9%
4167763 2002.1.1.0 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.65 50.0 2.90e-01 100.0% 8.6%
4299866 103.5.1.4 ↗ alpha arrays › RuvA-C › post-HMGL domain-like › post-HMGL domain-like › HCS_D2 0.64 52.0 4.51e-01 100.0% 55.0%
D2 medium residues 46-96
PDB
Domain cluster: rep: putative_nucleic_acid_binding_protein__YP_002574619__Helleborus_net_necrosis_virus__592206__D46-93
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01623.24 best Carla_C4 81.4 6.10e-23 96.1% 51.6%