←Back to structures

DNA_ligase

Euk-Vir

Acanthamoeba_polyphaga_mimivirus

DNA_ligase__YP_003986805__Acanthamoeba_polyphaga_mimivirus__212035

Identity

Accession:
YP_003986805 ↗
Protein ID:
DNA_ligase
Kingdom:
euk

Quality

83.7 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Megaviricetes› Imitervirales› Mimiviridae› Mimivirus› Acanthamoeba_polyphaga_mimivirus

TaxID: 212035

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 1-79
PDB
D2 high residues 298-381
PDB
Domain cluster: rep: LC680885.1__BDE75744.1__X__00206__D318-424
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03120.23 best OB_DNA_ligase 37.7 2.30e-09 92.9% 93.7%
D3 high residues 569-634
PDB
Domain cluster: rep: MN095770.1__QFR57709.1__CPT_Slocum_152__00129__D178-251
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF00533.34 best BRCT 42.6 8.00e-11 93.9% 76.9%
PF12738.14 PTCB-BRCT 28.4 1.90e-06 90.9% 73.0%
D4 medium residues 85-115_240-293
PDB
Domain cluster: rep: ON649702__UVF62572.1__X__00095__D231-262_382-434
CATH (31)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6kduA02 3.30.470.30 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › DNA ligase/mRNA capping enzyme 0.83 77.0 5.39e-01 100.0% 94.0%
1b04A02 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.83 76.0 7.22e-01 98.8% 98.0%
1dgsA02 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.81 72.0 6.95e-01 95.3% 100.0%
1x9nA02 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.79 66.0 6.67e-01 97.6% 91.7%
3l2pA02 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.76 59.0 6.38e-01 98.8% 100.0%
5d1oA02 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.76 61.0 6.47e-01 97.6% 100.0%
2vugA02 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.75 60.0 6.42e-01 97.6% 100.0%
1fviA01 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.75 61.0 6.27e-01 97.6% 93.7%
3kyhC01 3.30.470.30 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › DNA ligase/mRNA capping enzyme 0.69 63.0 4.50e-01 100.0% 85.4%
3ty5A01 3.30.470.30 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › DNA ligase/mRNA capping enzyme 0.67 61.0 4.07e-01 100.0% 71.3%
3glkA03 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.66 45.0 5.07e-01 74.1% 100.0%
1xdnA01 3.30.1490.70 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › 0.65 58.0 5.34e-01 100.0% 89.1%
1xk5A01 3.30.470.30 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › DNA ligase/mRNA capping enzyme 0.63 57.0 4.32e-01 100.0% 89.4%
3gidB02 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.63 46.0 4.65e-01 77.6% 98.8%
1vkzA02 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.62 44.0 4.77e-01 76.5% 97.1%
3au4A02 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.61 45.0 4.39e-01 80.0% 89.4%
2r7kA03 3.30.1490.20 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › ATP-grasp fold, A domain 0.60 40.0 4.50e-01 76.5% 95.1%
1wi0A00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.59 44.0 4.06e-01 80.0% 73.5%
5bviA00 2.60.200.10 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.56 49.0 3.88e-01 100.0% 81.3%
2cs4A00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.55 42.0 4.07e-01 81.2% 77.9%
3w3sA01 3.30.70.1920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 38.0 3.04e-01 71.8% 82.7%
4y5tB00 2.60.120.620 Mainly Beta › Sandwich › Jelly Rolls › q2cbj1_9rhob like domain 0.54 38.0 2.68e-01 74.1% 85.6%
2o8rB02 3.30.1840.10 Alpha Beta › 2-Layer Sandwich › polyphosphate kinase like › Polyphosphate kinase middle domain 0.54 44.0 3.64e-01 89.4% 91.6%
5optn00 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 0.54 29.0 2.89e-01 92.9% 45.2%
3dshA01 2.60.200.10 Mainly Beta › Sandwich › Tumour Suppressor Smad4 › 0.53 47.0 3.60e-01 100.0% 80.7%
2dymC01 3.10.20.620 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.53 39.0 3.76e-01 80.0% 73.3%
3vthA02 3.30.110.120 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › 0.52 33.0 3.51e-01 95.3% 73.3%
4a55A01 3.10.20.770 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.52 38.0 2.68e-01 80.0% 28.7%
2v72A00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.51 43.0 3.82e-01 98.8% 89.8%
3onhA01 3.10.290.20 Alpha Beta › Roll › Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A › Ubiquitin-like 2 activating enzyme e1b. Chain: B, domain 3 0.51 44.0 4.09e-01 97.6% 79.3%
8d3mI01 3.90.320.10 Alpha Beta › Alpha-Beta Complex › Lambda Exonuclease; Chain A › 0.50 36.0 2.78e-01 76.5% 56.0%
ECOD (34)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4323403 206.1.3.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.85 79.0 5.31e-01 100.0% 76.6%
4432215 206.1.3.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.84 78.0 5.16e-01 100.0% 74.2%
4160069 206.1.3.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.84 78.0 5.14e-01 100.0% 74.2%
3840047 206.1.3.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.84 77.0 5.13e-01 100.0% 73.5%
4265994 206.1.3.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.83 77.0 5.09e-01 100.0% 74.2%
4566687 206.1.3.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp 0.83 77.0 5.06e-01 100.0% 71.1%
4321612 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 0.82 76.0 5.29e-01 100.0% 93.7%
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 0.75 68.0 4.27e-01 100.0% 49.2%
3927529 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 68.0 4.88e-01 100.0% 91.3%
3495502 206.1.3.4 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › mRNA_cap_enzyme 0.68 61.0 4.25e-01 100.0% 79.9%
3397951 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 0.68 60.0 3.76e-01 100.0% 42.9%
3878834 206.1.3.30 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › SPN1_m3Gcap_bd 0.63 57.0 4.06e-01 100.0% 71.6%
3550572 206.1.3.30 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › SPN1_m3Gcap_bd 0.63 57.0 4.00e-01 100.0% 68.5%
1392732 221.1.1.4 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PB1 0.60 44.0 4.04e-01 78.8% 71.3%
5048876 3986.2.1.0 ↗ a+b two layers › GTP-binding protein lepA C-terminal domain-like › Antitoxin Dmd › Antitoxin Dmd 0.59 42.0 4.63e-01 75.3% 96.9%
3552093 11.1.1.234 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › RET_CLD1 0.59 51.0 4.52e-01 100.0% 90.0%
3292295 221.1.1.4 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PB1 0.59 43.0 4.19e-01 78.8% 75.8%
4993947 309.1.2.2 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_bind_4 0.59 44.0 3.52e-01 80.0% 87.6%
3686690 304.3.1.1 ↗ a+b two layers › Alpha-beta plaits › HMA-related › HMA, heavy metal-associated domain › HMA 0.57 41.0 4.10e-01 75.3% 100.0%
3470623 73.1.1.6 ↗ beta sandwiches › SMAD/FHA domain › SMAD/FHA domain › SMAD/FHA domain › IRF-3 0.56 48.0 3.76e-01 100.0% 77.5%
4014325 376.1.1.0 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.56 34.0 3.70e-01 72.9% 74.3%
3637145 376.1.1.21 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_2 0.56 36.0 3.56e-01 72.9% 61.1%
4996591 309.1.2.2 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_bind_4 0.55 40.0 3.17e-01 77.6% 82.3%
3172253 2004.1.1.212 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Microtub_bd 0.54 47.0 3.12e-01 100.0% 23.9%
3553026 221.1.1.4 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PB1 0.54 39.0 3.86e-01 78.8% 73.7%
2142307 73.1.1.6 ↗ beta sandwiches › SMAD/FHA domain › SMAD/FHA domain › SMAD/FHA domain › IRF-3 0.54 47.0 3.73e-01 100.0% 76.2%
3273867 221.1.1.4 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › PB1 0.52 38.0 3.82e-01 75.3% 91.8%
3914798 73.1.1.6 ↗ beta sandwiches › SMAD/FHA domain › SMAD/FHA domain › SMAD/FHA domain › IRF-3 0.52 46.0 3.54e-01 100.0% 82.0%
3997556 386.1.1.24 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-C2H2_4 0.52 44.0 3.15e-01 100.0% 63.7%
3237024 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.52 39.0 3.52e-01 81.2% 65.8%
3702709 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.52 39.0 3.85e-01 81.2% 81.1%
5041620 2492.1.1.18 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › Prok-JAB 0.52 46.0 3.36e-01 97.6% 47.1%
3890764 386.1.1.1 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-C2H2 0.52 34.0 3.41e-01 75.3% 64.4%
5000854 309.1.2.2 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_bind_4 0.51 36.0 3.02e-01 74.1% 87.7%
D5 medium residues 116-239
PDB
Domain cluster: rep: DNA_polymerase_X_NAD-dependent_DNA_ligase_fusion_protein__YP_009173744__Chrysochromulina_ericina_virus__455364__D566-656
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01653.24 best DNA_ligase_aden 48.8 9.70e-13 100.0% 54.1%
D6 medium residues 400-548
PDB
Domain cluster: rep: NAD-dependent_DNA_ligase__YP_010084817__Shrimp_hemocyte_iridescent_virus__2039780__D372-518