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NAD-dependent_DNA_ligase

Euk-Vir

Choristoneura_rosaceana_entomopoxvirus_L

NAD-dependent_DNA_ligase__YP_008004602__Choristoneura_rosaceana_entomopoxvirus_L__1293539

Identity

Accession:
YP_008004602 ↗
Protein ID:
NAD-dependent_DNA_ligase
Kingdom:
euk

Quality

83.5 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Pokkesviricetes› Chitovirales› Poxviridae› Betaentomopoxvirus› Choristoneura_rosaceana_entomopoxvirus_'L'

TaxID: 1293539

Cluster

View cluster (18 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 1-71
PDB
Domain cluster: representative
CATH (47)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1fnnB03 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 0.72 50.0 4.42e-01 73.2% 100.0%
4a17U01 1.10.287.310 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.69 51.0 5.03e-01 78.9% 85.7%
3feyA02 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.69 59.0 4.40e-01 100.0% 43.8%
2qyuA02 1.25.40.300 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Putative secreted effector protein 0.69 60.0 4.43e-01 100.0% 37.9%
1nktA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.67 51.0 3.38e-01 81.7% 51.2%
4xvxA01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.65 51.0 4.46e-01 87.3% 73.0%
4i1eA03 1.25.10.30 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › IP3 receptor type 1 binding core, RIH domain 0.65 50.0 4.06e-01 84.5% 98.6%
1y6xA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.64 48.0 4.48e-01 78.9% 72.4%
2wzkA01 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.64 45.0 3.78e-01 74.6% 91.3%
4gltA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.64 54.0 4.65e-01 95.8% 78.9%
3j27A05 1.20.1280.260 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.63 43.0 3.86e-01 70.4% 51.0%
4irnA01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.63 50.0 4.28e-01 88.7% 72.3%
3c8eA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.63 51.0 4.05e-01 93.0% 54.1%
1lvfB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 49.0 4.29e-01 84.5% 90.4%
3r2qA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.62 52.0 4.53e-01 94.4% 82.3%
1s05A00 1.20.120.10 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c/b562 0.62 43.0 3.60e-01 73.2% 79.8%
3n71A03 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.62 50.0 3.66e-01 93.0% 32.9%
2xi5A00 3.40.91.60 Alpha Beta › 3-Layer(aba) Sandwich › Restriction Endonuclease › 0.61 47.0 3.54e-01 84.5% 96.7%
1vq8V00 1.10.287.310 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.61 42.0 4.34e-01 71.8% 92.3%
3mekA04 1.25.40.970 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.61 49.0 4.81e-01 91.5% 83.7%
2e9xD01 1.20.58.1030 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 48.0 3.96e-01 90.1% 82.5%
2e2eA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.60 46.0 3.66e-01 100.0% 39.7%
7nc3F01 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.60 50.0 4.37e-01 95.8% 80.7%
1hqoA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.60 48.0 4.07e-01 93.0% 80.2%
1ryp200 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.60 41.0 2.90e-01 71.8% 57.5%
1sqgA01 1.10.940.10 Mainly Alpha › Orthogonal Bundle › N-utilizing Substance Protein B Homolog; Chain A › NusB-like 0.60 40.0 3.24e-01 73.2% 35.5%
2fbnA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.60 51.0 4.05e-01 97.2% 60.1%
2v6yA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.59 47.0 4.67e-01 87.3% 89.3%
4egwA02 1.20.58.340 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Magnesium transport protein CorA, transmembrane region 0.59 45.0 3.87e-01 84.5% 84.9%
4ri6A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.59 51.0 4.37e-01 100.0% 84.0%
4ivfA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.59 48.0 4.17e-01 94.4% 87.1%
4l8eA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.59 48.0 4.25e-01 94.4% 87.3%
2yxhA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.58 41.0 3.62e-01 74.6% 61.1%
3c1dA03 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 0.58 32.0 3.87e-01 74.6% 82.6%
4a15A03 1.10.275.40 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › 0.58 44.0 3.67e-01 85.9% 68.6%
5an3A01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.57 50.0 4.16e-01 100.0% 58.9%
6a3kA00 1.20.120.10 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c/b562 0.57 41.0 3.50e-01 80.3% 100.0%
1udyA01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.56 44.0 3.84e-01 91.5% 94.2%
2a9uA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.55 47.0 3.96e-01 97.2% 62.7%
1t5oA01 1.20.120.420 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › translation initiation factor eif-2b, domain 1 0.55 48.0 3.90e-01 100.0% 64.5%
1t9kA01 1.20.120.420 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › translation initiation factor eif-2b, domain 1 0.54 47.0 3.84e-01 100.0% 63.6%
2xl4A00 1.20.120.1420 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › LntA helical domain 0.54 44.0 3.54e-01 91.5% 63.9%
3k1hA00 3.30.1120.180 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › Flagellar FLiS export co-chaperone, HP1076 0.52 40.0 3.49e-01 84.5% 91.3%
5domA00 1.10.110.10 Mainly Alpha › Orthogonal Bundle › Hydrophobic Seed Protein › Plant lipid-transfer and hydrophobic proteins 0.51 42.0 4.04e-01 100.0% 93.3%
4cgyA02 1.10.460.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; domain 2 › Topoisomerase I, domain 2 0.51 40.0 3.04e-01 88.7% 53.7%
2ds2D01 1.10.110.10 Mainly Alpha › Orthogonal Bundle › Hydrophobic Seed Protein › Plant lipid-transfer and hydrophobic proteins 0.51 35.0 3.76e-01 71.8% 93.0%
6pw7A02 1.10.150.50 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Transcription Factor, Ets-1 0.50 37.0 3.74e-01 78.9% 88.7%
ECOD (33)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4360726 206.1.3.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.80 69.0 4.53e-01 100.0% 23.4%
4323403 206.1.3.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.77 56.0 3.63e-01 76.1% 39.3%
4411335 206.1.3.5 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › DNA_ligase_aden 0.77 69.0 4.49e-01 100.0% 46.3%
3278752 206.1.3.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.74 53.0 3.48e-01 76.1% 20.7%
3314581 4207.1.2.0 ↗ alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › MED7 hinge region 0.73 58.0 5.18e-01 87.3% 64.0%
3714029 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.70 49.0 3.55e-01 71.8% 93.7%
3277363 601.4.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.66 46.0 3.76e-01 73.2% 79.3%
4000674 109.4.1.20 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › RYDR_ITPR 0.65 57.0 4.00e-01 100.0% 58.7%
3498760 109.4.1.173 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › NatA_aux_su 0.64 57.0 3.51e-01 100.0% 32.5%
4600893 4121.1.1.0 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like 0.64 53.0 3.64e-01 93.0% 59.2%
4985812 109.47.1.1 ↗ alpha superhelices › Repetitive alpha hairpins › Helical C-terminal domain in magnesium chelatase catalytic subunit › Helical C-terminal domain in magnesium chelatase catalytic subunit › CobN-Mg_chel 0.64 55.0 4.45e-01 100.0% 91.0%
3695389 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.64 53.0 3.80e-01 98.6% 66.3%
3275970 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.63 54.0 3.15e-01 100.0% 15.2%
3958744 604.24.1.1 ↗ alpha bundles › Spectrin repeat-like › Helical bundle domain in putative transcriptional regulator Jann_0659-related proteins › Helical bundle domain in putative transcriptional regulator Jann_0659-related proteins › PaaX_C 0.63 55.0 4.95e-01 98.6% 90.0%
1308183 109.4.1.20 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › RYDR_ITPR 0.63 48.0 3.79e-01 85.9% 75.5%
3781682 650.1.1.1 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › DnaJ 0.62 42.0 4.10e-01 70.4% 67.5%
3615373 650.1.1.0 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain 0.62 42.0 3.53e-01 70.4% 43.2%
3591967 650.1.1.0 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain 0.62 42.0 3.98e-01 70.4% 63.5%
3253882 109.1.1.6 ↗ alpha superhelices › Repetitive alpha hairpins › Glutathione S-transferase (GST)-C › Glutathione S-transferase (GST)-C › GST_C_2 0.61 52.0 4.34e-01 100.0% 76.3%
4028117 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.60 50.0 3.36e-01 97.2% 36.8%
3597463 650.1.1.0 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain 0.59 41.0 4.00e-01 71.8% 77.5%
3245665 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 0.58 39.0 4.00e-01 70.4% 87.1%
3618531 3923.1.1.1 ↗ alpha bundles › Mitotic chromosome determinant-related protein N-terminal domain › Mitotic chromosome determinant-related protein N-terminal domain › Mitotic chromosome determinant-related protein N-terminal domain › Rad21_Rec8_N 0.58 46.0 4.21e-01 87.3% 78.9%
3579205 192.4.1.25 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) › Rad21_Rec8_N 0.58 41.0 3.72e-01 73.2% 68.4%
3885624 186.1.1.0 ↗ alpha arrays › lambda integrase-N-like › lambda integrase-N › lambda integrase-N 0.58 46.0 3.92e-01 87.3% 75.0%
3238459 616.1.1.0 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain 0.58 46.0 4.77e-01 100.0% 93.8%
3182808 650.1.1.1 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › DnaJ 0.58 39.0 4.04e-01 70.4% 86.2%
3403421 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.57 50.0 3.99e-01 100.0% 60.1%
3726017 633.15.1.1 ↗ alpha bundles › Bromodomain-like › alpha-ketoacid dehydrogenase kinase-N › alpha-ketoacid dehydrogenase kinase-N › BCDHK_Adom3 0.57 43.0 3.26e-01 83.1% 86.5%
4970947 606.1.1.0 ↗ alpha complex topology › Nop N-terminal domain › Nop N-terminal domain › Nop N-terminal domain 0.56 42.0 3.47e-01 84.5% 45.5%
3992502 509.1.1.1 ↗ alpha bundles › PAH2 domain › PAH2 domain › PAH2 domain › PAH 0.54 37.0 3.47e-01 71.8% 58.9%
5072101 3651.1.1.1 ↗ alpha bundles › Translation initiation factor eIF-2B delta subunit N-terminal helical domain › Translation initiation factor eIF-2B delta subunit N-terminal helical domain › Translation initiation factor eIF-2B delta subunit N-terminal helical domain › IF-2B 0.54 45.0 3.94e-01 97.2% 100.0%
3880261 5000.3.1.0 ↗ alpha arrays › Toxins' membrane translocation domains › Bcl-2 inhibitors of programmed cell death › Bcl-2 inhibitors of programmed cell death 0.50 40.0 3.07e-01 93.0% 78.9%
D2 high residues 290-381
PDB
Domain cluster: rep: LC680885.1__BDE75744.1__X__00206__D318-424
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03120.23 best OB_DNA_ligase 37.4 2.80e-09 83.7% 93.7%
D3 medium residues 72-82_116-228
PDB
Domain cluster: rep: DNA_polymerase_X_NAD-dependent_DNA_ligase_fusion_protein__YP_009173744__Chrysochromulina_ericina_virus__455364__D566-656
D4 medium residues 83-115_229-287
PDB
Domain cluster: rep: ON649702__UVF62572.1__X__00095__D231-262_382-434
D5 medium residues 387-526
PDB
Domain cluster: rep: NAD-dependent_DNA_ligase__YP_010084817__Shrimp_hemocyte_iridescent_virus__2039780__D372-518