←Back to structures

DNA-ligase

Euk-Vir

Diatraea_saccharalis_granulovirus

DNA-ligase__YP_009182307__Diatraea_saccharalis_granulovirus__1675862

Identity

Accession:
YP_009182307 ↗
Protein ID:
DNA-ligase
Kingdom:
euk

Quality

77.1 mean pLDDT

Taxonomy

Naldaviricetes› Lefavirales› Baculoviridae› Betabaculovirus› Diatraea_saccharalis_granulovirus

TaxID: 1675862

Cluster

Singleton — not in a non-trivial cluster

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 3-155
PDB
Domain cluster: rep: DNA_ligase__YP_009329768__BeAn_58058_virus__67082__D5-155
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF04675.20 best DNA_ligase_A_N 25.4 2.00e-05 96.7% 88.5%
CATH (5)
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 0.81 77.0 6.99e-01 100.0% 79.3%
3gdeA01 1.10.3260.10 Mainly Alpha › Orthogonal Bundle › DNA ligase i, domain 1 › DNA ligase, ATP-dependent, N-terminal domain 0.77 72.0 6.25e-01 100.0% 74.6%
4htpB00 1.10.3260.10 Mainly Alpha › Orthogonal Bundle › DNA ligase i, domain 1 › DNA ligase, ATP-dependent, N-terminal domain 0.74 69.0 6.03e-01 100.0% 79.7%
1x9nA01 1.10.3260.10 Mainly Alpha › Orthogonal Bundle › DNA ligase i, domain 1 › DNA ligase, ATP-dependent, N-terminal domain 0.74 69.0 5.60e-01 100.0% 57.8%
2gnoA03 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.65 27.0 3.29e-01 97.4% 56.0%
ECOD (20)
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 0.82 79.0 7.22e-01 100.0% 82.1%
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 0.82 78.0 5.51e-01 100.0% 37.4%
4417241 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 76.0 6.56e-01 100.0% 77.3%
4932787 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 0.79 75.0 6.58e-01 100.0% 77.2%
3783063 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 0.79 74.0 6.40e-01 99.3% 84.0%
3730297 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 0.79 74.0 6.07e-01 100.0% 75.5%
3633373 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 0.79 74.0 5.13e-01 100.0% 38.1%
3315181 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 0.77 72.0 5.97e-01 100.0% 64.6%
4066585 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 0.77 73.0 6.40e-01 100.0% 74.0%
5029809 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 0.77 72.0 6.04e-01 100.0% 66.0%
3738749 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 0.77 72.0 5.88e-01 100.0% 62.2%
5046138 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 0.77 72.0 6.32e-01 100.0% 75.5%
4597196 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 0.77 72.0 6.44e-01 100.0% 78.0%
4966635 4095.1.1.0 ↗ alpha bundles › ATP-dependent DNA ligase DNA-binding domain › ATP-dependent DNA ligase DNA-binding domain › ATP-dependent DNA ligase DNA-binding domain 0.77 72.0 6.85e-01 100.0% 93.7%
4189730 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 0.76 71.0 6.27e-01 100.0% 77.2%
3704757 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 0.76 70.0 6.45e-01 99.3% 83.1%
4951306 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 0.75 70.0 5.03e-01 100.0% 40.0%
3923254 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 0.74 69.0 6.52e-01 100.0% 89.4%
3939304 4095.1.1.3 ↗ 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 0.73 69.0 4.84e-01 100.0% 36.2%
4983230 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 0.66 57.0 5.42e-01 100.0% 78.3%
D2 high residues 196-364
PDB
Domain cluster: rep: Salt_Pond_R1_B_H2O_MG_scaffold_1_prodigal-single.1__X__X__00295__D161-347
Pfam (3)
AccessionNameScoreE-valueQ covHMM cov
PF09414.16 best RNA_ligase 44.4 2.80e-11 92.3% 98.2%
PF01068.27 DNA_ligase_A_M 68.6 8.70e-19 53.8% 44.1%
PF01068.27 DNA_ligase_A_M 40.5 3.40e-10 48.5% 39.7%
D3 high residues 369-531
PDB
Domain cluster: rep: DNA_ligase_-2-__YP_010377156__Monkeypox_virus__10244__D413-557