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dna_ligase

Euk-Vir

Sucra_jujuba_nucleopolyhedrovirus

dna_ligase__YP_009186741__Sucra_jujuba_nucleopolyhedrovirus__1563660

Identity

Accession:
YP_009186741 ↗
Protein ID:
dna_ligase
Kingdom:
euk

Quality

71.9 mean pLDDT

Taxonomy

Naldaviricetes› Lefavirales› Baculoviridae› Alphabaculovirus› Sucra_jujuba_nucleopolyhedrovirus

TaxID: 1563660

Cluster

View cluster (36 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 449-597
PDB
Domain cluster: rep: DNA_ligase_-2-__YP_010377156__Monkeypox_virus__10244__D413-557
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF04679.22 best DNA_ligase_A_C 54.8 1.40e-14 75.8% 98.9%
D2 medium residues 117-198
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF04675.20 best DNA_ligase_A_N 36.3 9.20e-09 74.4% 35.6%
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3l2pA01 1.10.3260.10 Mainly Alpha › Orthogonal Bundle › DNA ligase i, domain 1 › DNA ligase, ATP-dependent, N-terminal domain 0.87 81.0 5.93e-01 100.0% 93.9%
2hivA01 1.10.3260.10 Mainly Alpha › Orthogonal Bundle › DNA ligase i, domain 1 › DNA ligase, ATP-dependent, N-terminal domain 0.82 75.0 5.43e-01 100.0% 91.7%
8amzP01 1.25.40.570 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.66 55.0 3.56e-01 92.7% 29.1%
1nktA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.64 47.0 3.26e-01 78.0% 55.7%
4eqyA02 1.20.1180.10 Mainly Alpha › Up-down Bundle › Udp N-acetylglucosamine O-acyltransferase; Domain 2 › Udp N-acetylglucosamine O-acyltransferase, C-terminal domain 0.61 41.0 4.39e-01 82.9% 81.4%
4crwA00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.61 48.0 3.60e-01 91.5% 32.3%
4uf1A00 1.10.437.10 Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › Blc2-like 0.61 50.0 4.31e-01 100.0% 56.3%
5haxA01 1.20.58.1780 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.59 52.0 3.79e-01 100.0% 83.1%
3w3uA01 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.59 52.0 2.93e-01 98.8% 10.9%
4hehA01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.59 51.0 5.13e-01 98.8% 95.2%
3rbtA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.59 48.0 4.30e-01 90.2% 88.0%
2dg8D00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.55 42.0 3.41e-01 84.1% 69.4%
4ap2B01 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.55 46.0 3.97e-01 93.9% 80.6%
2a2fX02 1.20.58.670 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Dsl1p vesicle tethering complex, Tip20p subunit, domain D 0.55 46.0 4.04e-01 96.3% 78.3%
4zhbA00 1.25.40.20 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Ankyrin repeat-containing domain 0.54 43.0 4.06e-01 89.0% 96.2%
3rcyB01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.54 38.0 3.25e-01 82.9% 43.3%
3ecsC01 1.20.120.1070 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Translation initiation factor eIF-2B, N-terminal domain 0.54 46.0 4.37e-01 97.6% 87.0%
2j9qB00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.53 45.0 3.25e-01 100.0% 48.7%
7nc3F01 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.52 42.0 3.84e-01 90.2% 95.6%
1g4uS01 1.20.120.260 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Virulence factor YopE uncharacterised domain 0.52 39.0 3.48e-01 82.9% 79.5%
7qx4A01 1.20.190.10 Mainly Alpha › Up-down Bundle › Delta-Endotoxin; domain 1 › Pesticidal crystal protein, N-terminal domain 0.52 45.0 3.31e-01 100.0% 47.9%
4bwrA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.52 41.0 2.61e-01 95.1% 15.2%
3e4bA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.51 43.0 2.84e-01 100.0% 33.4%
1p8dB00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.50 43.0 3.16e-01 100.0% 87.0%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3253689 4095.1.1.1 ↗ alpha bundles › ATP-dependent DNA ligase DNA-binding domain › ATP-dependent DNA ligase DNA-binding domain › ATP-dependent DNA ligase DNA-binding domain › DNA_ligase_A_N 0.89 84.0 6.21e-01 100.0% 97.9%
5072397 4095.1.1.1 ↗ alpha bundles › ATP-dependent DNA ligase DNA-binding domain › ATP-dependent DNA ligase DNA-binding domain › ATP-dependent DNA ligase DNA-binding domain › DNA_ligase_A_N 0.80 72.0 6.60e-01 98.8% 94.3%
3395961 613.1.1.1 ↗ alpha complex topology › Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) › Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) › Putative anticodon-binding domain of alanyl-tRNA synthetase (AlaRS) › tRNA-synt_2c 0.67 49.0 3.62e-01 78.0% 37.8%
3434578 109.4.1.32 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › MIF4G 0.63 53.0 4.83e-01 92.7% 69.1%
3648891 109.4.1.420 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR 0.63 50.0 3.98e-01 89.0% 58.9%
3936544 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.63 50.0 4.18e-01 89.0% 74.7%
3326892 109.4.1.1305 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, PPR_long, TPR_24 0.60 51.0 2.98e-01 97.6% 12.8%
4983142 101.8.1.2 ↗ alpha arrays › HTH › An anticodon-binding domain of class I aminoacyl-tRNA synthetases › An anticodon-binding domain of class I aminoacyl-tRNA synthetases › Anticodon_2 0.58 44.0 3.48e-01 82.9% 37.2%
3188696 109.4.1.501 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › UME 0.58 48.0 2.84e-01 92.7% 39.3%
3589439 1179.1.1.1 ↗ alpha complex topology › TelC toxin domain › TelC toxin domain › TelC toxin domain › YkzU 0.58 48.0 3.40e-01 92.7% 62.6%
4939044 109.4.1.207 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HEAT_2 0.57 44.0 3.78e-01 97.6% 51.1%
3977859 109.4.1.109 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Sel1 0.57 44.0 3.85e-01 91.5% 54.4%
5061366 3636.1.1.0 ↗ a+b two layers › XPD arch domain › XPD arch domain › XPD arch domain 0.57 43.0 3.77e-01 82.9% 82.3%
3659961 109.4.1.1779 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, PPR_3 0.56 41.0 3.46e-01 97.6% 43.3%
3512399 109.4.1.109 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Sel1 0.56 41.0 3.32e-01 96.3% 38.2%
3507662 109.54.1.1 ↗ alpha superhelices › Repetitive alpha hairpins › C-terminal tetramerization domain of Utp1/Utp21/Utp12/Utp13 › C-terminal tetramerization domain of Utp1/Utp21/Utp12/Utp13 › Utp12 0.55 45.0 3.83e-01 90.2% 72.9%
3609865 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.55 45.0 3.70e-01 96.3% 46.1%
1509102 109.4.1.1803 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Sel1, PF27483 0.55 42.0 2.80e-01 86.6% 18.0%
4854884 4963.1.2.1 ↗ alpha complex topology › N-terminal additional helical subdomain in reovirus polymerase lambda3 › N-terminal additional helical subdomain in reovirus polymerase lambda3 › N-terminal domain in vesicular stomatitis virus RNA polymerase L › Mononeg_RNA_pol 0.55 41.0 3.23e-01 80.5% 63.6%
4256843 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.53 38.0 3.43e-01 91.5% 52.5%
3875617 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.52 44.0 2.58e-01 100.0% 45.3%
4799140 109.4.1.109 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Sel1 0.52 38.0 4.19e-01 87.8% 100.0%
3337409 109.4.1.1277 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR_1, PPR_2, TPR_24 0.52 45.0 3.83e-01 97.6% 71.1%
3356624 109.4.1.109 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Sel1 0.52 40.0 3.46e-01 95.1% 52.3%
3590383 5082.1.1.1 ↗ alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation_efflux 0.52 42.0 3.14e-01 87.8% 87.5%
3668969 109.4.1.1272 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, E_motif 0.51 43.0 2.96e-01 98.8% 30.9%
3458691 109.4.1.420 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR 0.51 41.0 3.51e-01 93.9% 51.7%
3909203 109.24.1.2 ↗ alpha superhelices › Repetitive alpha hairpins › Helical domain in dedicator of cytokinesis protein 9 › Helical domain in dedicator of cytokinesis protein 9 › DHR-2_Lobe_C 0.51 42.0 3.69e-01 92.7% 92.0%
3325847 109.4.1.1269 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, E_motif 0.50 42.0 3.35e-01 97.6% 47.9%
D3 medium residues 230-284_347-442
PDB
Domain cluster: rep: Salt_Pond_R1_B_H2O_MG_scaffold_1_prodigal-single.1__X__X__00295__D161-347
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF01068.27 best DNA_ligase_A_M 82.2 6.00e-23 60.9% 43.1%
PF01068.27 DNA_ligase_A_M 55.7 7.70e-15 32.5% 24.0%
D4 medium residues 285-346
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01068.27 best DNA_ligase_A_M 26.4 7.10e-06 100.0% 21.1%
CATH (13)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3l2pA03 3.30.470.30 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › DNA ligase/mRNA capping enzyme 0.90 83.0 6.51e-01 100.0% 51.7%
2incC00 3.10.20.270 Alpha Beta › Roll › Ubiquitin-like (UB roll) › TmoB-like 0.63 51.0 4.67e-01 95.2% 68.7%
1twfB08 3.90.1800.10 Alpha Beta › Alpha-Beta Complex › DCoH-like › RNA polymerase alpha subunit dimerisation domain 0.60 42.0 3.75e-01 72.6% 61.2%
6x4tA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.56 46.0 4.22e-01 93.5% 82.4%
2dzkA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.56 42.0 3.99e-01 93.5% 68.8%
2c7hA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.55 39.0 3.58e-01 95.2% 55.8%
3h7lA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 45.0 3.99e-01 93.5% 71.0%
2b9lA01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.54 40.0 3.07e-01 82.3% 42.7%
2bpsA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.54 41.0 3.88e-01 91.9% 67.9%
3vqiA01 3.10.20.620 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.53 41.0 3.61e-01 96.8% 53.7%
3x17A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 42.0 3.68e-01 95.2% 71.6%
1wgrA01 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.50 40.0 3.74e-01 95.2% 75.6%
2v1yA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.50 40.0 3.70e-01 96.8% 67.4%
ECOD (19)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3581071 4095.1.1.2 ↗ alpha bundles › ATP-dependent DNA ligase DNA-binding domain › ATP-dependent DNA ligase DNA-binding domain › ATP-dependent DNA ligase DNA-binding domain › DNA_ligase_A_M+DNA_ligase_A_N 0.93 87.0 5.07e-01 100.0% 14.6%
3799247 206.1.3.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.92 86.0 5.45e-01 100.0% 23.8%
3795817 206.1.3.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › DNA_ligase_A_M 0.91 84.0 5.36e-01 100.0% 23.4%
3709350 304.31.1.0 ↗ a+b two layers › Alpha-beta plaits › HMG-CoA reductase › NAD-binding domain of HMG-CoA reductase 0.60 47.0 3.42e-01 87.1% 94.4%
3522555 221.1.1.7 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › UBX 0.57 45.0 4.05e-01 93.5% 60.0%
3882310 221.1.1.61 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › Kindlin_2_N 0.56 41.0 3.83e-01 95.2% 61.2%
3531830 11.1.1.363 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C2-set_3 0.55 46.0 3.85e-01 93.5% 67.3%
3265036 221.1.1.76 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.55 43.0 4.03e-01 93.5% 76.5%
3483582 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.55 43.0 3.84e-01 93.5% 58.0%
3737908 221.1.1.94 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › AIP3 0.54 40.0 3.79e-01 96.8% 65.0%
3477612 221.1.1.61 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › Kindlin_2_N 0.54 40.0 3.55e-01 95.2% 52.0%
3836831 221.1.1.7 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › UBX 0.54 40.0 3.69e-01 93.5% 58.9%
3490660 221.1.1.76 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RA_2 0.53 43.0 3.68e-01 93.5% 74.3%
2390911 11.1.1.48 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › CelD_N 0.53 43.0 3.86e-01 91.9% 70.7%
3928043 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.53 43.0 3.91e-01 93.5% 70.0%
3409988 11.1.1.97 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › I-set 0.52 43.0 3.60e-01 93.5% 70.0%
5079246 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.52 43.0 3.79e-01 95.2% 66.3%
4231688 1.1.7.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.51 42.0 3.63e-01 91.9% 81.0%
3260557 221.1.1.56 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › FERM_f0 0.50 39.0 3.79e-01 91.9% 100.0%