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nucleic_acid_binding_protein

Euk-Vir

Phlox_virus_B

nucleic_acid_binding_protein__YP_001552322__Phlox_virus_B__475777

Identity

Accession:
YP_001552322 ↗
Protein ID:
nucleic_acid_binding_protein
Kingdom:
euk

Quality

72.8 mean pLDDT

Taxonomy

Orthornavirae› Kitrinoviricota› Alsuviricetes› Tymovirales› Betaflexiviridae› Carlavirus› Phlox_virus_B

TaxID: 475777

Cluster

View cluster (10 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 high residues 3-50
PDB
Domain cluster: representative
CATH (35)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3l9wA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.95 84.0 5.60e-01 95.8% 28.2%
1ls1A01 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.92 78.0 6.16e-01 89.6% 48.3%
1tj7A03 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.86 62.0 5.44e-01 83.3% 52.1%
1dcnA03 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.85 64.0 5.57e-01 83.3% 54.2%
4nleA03 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.85 71.0 6.02e-01 91.7% 59.2%
2rn7A01 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 0.83 58.0 5.15e-01 72.9% 53.0%
3jr7A01 3.40.50.10440 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Dihydroxyacetone kinase; domain 1 0.80 55.0 4.13e-01 72.9% 29.7%
3ibyD02 1.10.287.1770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.80 63.0 5.19e-01 85.4% 77.4%
6m36O01 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.79 62.0 5.03e-01 89.6% 44.8%
2fp1B00 1.20.59.10 Mainly Alpha › Up-down Bundle › Chorismate Mutase Domain, subunit A › Chorismate mutase 0.78 66.0 4.63e-01 100.0% 29.9%
3c3dA02 1.10.8.240 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › CofD-like domain 0.78 54.0 4.37e-01 72.9% 64.8%
1r1dA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.77 56.0 3.55e-01 81.2% 15.7%
7s0rB01 1.20.81.20 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › 0.76 65.0 5.62e-01 97.9% 64.5%
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 0.76 56.0 5.22e-01 79.2% 65.0%
1ss3A00 1.10.287.720 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Pollen allergen ole e 6 0.76 54.0 5.33e-01 75.0% 72.0%
2i5uA00 1.10.10.630 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › DnaD domain-like 0.75 58.0 4.92e-01 83.3% 55.8%
2ddmB00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.75 61.0 3.80e-01 93.8% 16.2%
3triA02 1.10.3730.10 Mainly Alpha › Orthogonal Bundle › ProC C-terminal domain-like fold › ProC C-terminal domain-like 0.74 63.0 4.98e-01 97.9% 47.6%
2q0yA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.74 59.0 4.20e-01 89.6% 30.4%
4fzwA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.71 51.0 4.89e-01 81.2% 65.5%
3vpxB02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.71 59.0 4.00e-01 100.0% 24.1%
2hh7A00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.71 62.0 5.06e-01 95.8% 62.4%
1tfeA02 1.10.286.20 Mainly Alpha › Orthogonal Bundle › GTP Cyclohydrolase I; Chain A, domain 1 › 0.70 54.0 5.52e-01 89.6% 93.3%
1xdxA01 3.30.1140.40 Alpha Beta › 2-Layer Sandwich › Ribosomal protein S3 C-terminal domain › Tctex-1 0.69 56.0 4.50e-01 93.8% 46.0%
5axmB00 3.30.70.3000 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › tRNA(His) guanylyltransferase (Thg1) 0.69 60.0 3.85e-01 100.0% 45.2%
1cxzB00 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.68 58.0 4.73e-01 95.8% 52.3%
4p17A02 1.10.8.270 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › putative rabgap domain of human tbc1 domain family member 14 like domains 0.68 53.0 4.07e-01 97.9% 37.3%
2pjqA01 1.10.472.50 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › HD-domain/PDEase-like 0.67 51.0 4.28e-01 91.7% 47.2%
5k3hB04 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.67 59.0 4.28e-01 100.0% 76.7%
2y4tA02 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.65 49.0 4.78e-01 89.6% 75.0%
6r1nA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.64 54.0 4.19e-01 93.8% 43.7%
2ddhA04 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.63 53.0 3.90e-01 95.8% 91.7%
1rr7A01 1.10.10.60 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Homeodomain-like 0.63 45.0 4.63e-01 89.6% 89.1%
2yevA02 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.57 51.0 4.44e-01 100.0% 64.9%
1rajA01 4.10.880.10 Few Secondary Structures › Irregular › Poliovirus 3D polymerase; domain 1 (Nucleotidyltransferase) › Poliovirus 3D polymerase Domain 1 (Nucleotidyltransferase) 0.55 38.0 4.02e-01 72.9% 81.8%
ECOD (36)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3483031 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.95 87.0 8.02e-01 100.0% 80.0%
4190679 2003.1.1.28 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › TrkA_N 0.93 81.0 5.09e-01 97.9% 20.9%
4032782 4125.1.1.0 ↗ alpha superhelices › BH3980-like › BH3980-like › BH3980-like 0.90 75.0 6.76e-01 91.7% 67.7%
3211845 103.1.1.0 ↗ alpha arrays › RuvA-C › RuvA-C, UBA, CRAL/TRIO-N, HBS1 › UBA-like domain 0.87 66.0 7.09e-01 83.3% 97.5%
5047182 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.87 79.0 7.10e-01 100.0% 76.9%
3708724 6026.1.1.0 ↗ alpha duplicates or obligate multimers › cwf21 domain › cwf21 domain › cwf21 domain 0.87 76.0 5.64e-01 100.0% 40.0%
4982432 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.85 77.0 6.44e-01 95.8% 61.3%
4981035 5058.1.1.16 ↗ 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 0.85 75.0 6.79e-01 100.0% 73.8%
4211233 4120.1.1.60 ↗ few secondary structure elements › Tim10/DDP › Tim10/DDP › Tim10/DDP › GlutR_dimer 0.84 74.0 6.27e-01 100.0% 70.0%
3234179 4953.1.1.0 ↗ beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like 0.83 69.0 5.89e-01 91.7% 57.3%
3463858 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.83 73.0 5.75e-01 100.0% 54.0%
3621479 6026.1.1.1 ↗ alpha duplicates or obligate multimers › cwf21 domain › cwf21 domain › cwf21 domain › cwf21 0.83 67.0 5.55e-01 89.6% 50.6%
3344802 6158.1.1.0 ↗ alpha bundles › Nucleoporin p58/p45 helical region › Nucleoporin p58/p45 helical region › Nucleoporin p58/p45 helical region 0.83 74.0 6.67e-01 100.0% 73.8%
2882139 129.1.1.4 ↗ alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › IlvC 0.81 67.0 4.51e-01 89.6% 28.0%
4990523 129.1.1.15 ↗ alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.81 64.0 5.02e-01 87.5% 43.2%
5060609 632.8.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 › alpha-2-Macroglobulin receptor associated protein (RAP) domain 1 0.81 71.0 6.15e-01 100.0% 69.3%
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) 0.79 64.0 5.98e-01 91.7% 71.7%
3682205 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.79 59.0 4.18e-01 81.2% 29.0%
4991198 2.1.1.359 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › HupF_HypC 0.79 66.0 5.11e-01 100.0% 45.2%
3685821 129.1.1.15 ↗ alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.78 66.0 5.01e-01 97.9% 40.0%
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 0.78 66.0 5.65e-01 100.0% 58.7%
4994798 3646.1.1.0 ↗ alpha complex topology › T-component of energy-coupling factor (ECF) transporters › T-component of energy-coupling factor (ECF) transporters › T-component of energy-coupling factor (ECF) transporters 0.78 67.0 4.41e-01 100.0% 24.5%
3286823 129.1.1.15 ↗ alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.77 64.0 4.77e-01 95.8% 37.5%
5032477 129.1.1.15 ↗ alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.75 63.0 4.84e-01 95.8% 40.9%
3643105 6026.1.1.1 ↗ alpha duplicates or obligate multimers › cwf21 domain › cwf21 domain › cwf21 domain › cwf21 0.75 65.0 4.61e-01 100.0% 31.0%
3764064 4009.1.1.0 ↗ alpha bundles › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins 0.74 63.0 5.27e-01 100.0% 55.3%
3881712 129.1.1.15 ↗ alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.73 60.0 4.36e-01 95.8% 33.3%
5024787 7064.1.1.0 ↗ alpha bundles › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 › Transmembrane domain of VIT1 0.73 59.0 4.18e-01 91.7% 98.7%
3476064 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.72 59.0 4.39e-01 93.8% 36.7%
3255785 129.1.1.15 ↗ alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › P5CR_dimer 0.72 60.0 4.63e-01 95.8% 45.5%
3474973 397.7.1.0 ↗ few secondary structure elements › Toxic hairpin › Ribosome-inactivating protein luffin P1 › Ribosome-inactivating protein luffin P1 0.71 56.0 5.43e-01 91.7% 83.6%
4682225 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 0.69 57.0 4.18e-01 100.0% 51.0%
5079848 5041.1.1.0 ↗ extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C 0.68 58.0 5.46e-01 100.0% 86.7%
3741234 605.2.1.3 ↗ alpha duplicates or obligate multimers › ROP-like › Hypothetical protein D-63 › Hypothetical protein D-63 › Seryl_tRNA_N 0.66 54.0 4.14e-01 93.8% 40.9%
4379 3014.1.1.1 ↗ alpha duplicates or obligate multimers › Middle operon regulator dimerization domain › Middle operon regulator dimerization domain › Middle operon regulator dimerization domain › Mor 0.63 45.0 4.63e-01 89.6% 89.1%
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 0.60 44.0 4.19e-01 83.3% 66.7%
D2 high residues 55-135
PDB
Domain cluster: rep: nucleic_acid_binding_protein__NP_659017__Garlic_virus_E__150285__D51-125
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF05515.17 best Viral_NABP 29.0 1.50e-06 90.1% 26.9%
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2p58C00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.57 44.0 4.02e-01 86.4% 61.6%
6z0fA02 1.25.40.680 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Type VII secretion system EssB, C-terminal-like domain 0.56 48.0 3.88e-01 98.8% 67.5%
2ijqA00 1.10.3450.10 Mainly Alpha › Orthogonal Bundle › Hyaluronidase domain-like › TTHA0068-like 0.56 44.0 3.62e-01 87.7% 47.6%
1iygA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.52 43.0 3.77e-01 95.1% 78.9%
3ll7A01 1.10.10.1110 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Methyltransferase PG1098, N-terminal domain 0.52 32.0 3.35e-01 85.2% 69.4%
4g75A01 1.20.1440.280 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.51 44.0 3.66e-01 100.0% 80.9%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3408927 109.4.1.33 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HEAT 0.65 45.0 2.69e-01 71.6% 27.8%
3677767 109.4.1.1991 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › CNOT1_CAF1_bind, HEAT_ULK4 0.57 46.0 3.05e-01 91.4% 42.2%
4945303 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.55 46.0 3.06e-01 93.8% 60.3%
3925346 109.3.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat 0.54 45.0 3.09e-01 95.1% 51.6%
4414070 109.4.1.179 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Nro1 0.54 45.0 3.33e-01 95.1% 45.7%
5018257 208.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded left-handed beta-helix › Trimeric LpxA-like enzymes › Trimeric LpxA-like enzymes 0.52 45.0 3.43e-01 100.0% 57.6%
3245771 109.4.1.155 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Med23 0.52 42.0 2.38e-01 93.8% 88.5%
3703252 101.1.10.0 ↗ alpha arrays › HTH › HTH › Cyclin-like 0.51 35.0 3.31e-01 82.7% 58.0%
3712332 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.51 45.0 3.49e-01 100.0% 88.3%
5025118 3843.1.1.1 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › Oxidored_q2 0.50 34.0 3.21e-01 70.4% 78.0%