←Back to structures

DNA_ligase

Euk-Vir

Penguinpox_virus

DNA_ligase__YP_009046044__Penguinpox_virus__648998

Identity

Accession:
YP_009046044 ↗
Protein ID:
DNA_ligase
Kingdom:
euk

Quality

84.5 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Pokkesviricetes› Chitovirales› Poxviridae› Avipoxvirus› Penguinpox_virus

TaxID: 648998

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 417-559
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 49.8 5.10e-13 76.2% 98.9%
D2 medium residues 1-53_162-204
PDB
Domain cluster: rep: dna_ligase__YP_009186741__Sucra_jujuba_nucleopolyhedrovirus__1563660__D117-198
CATH (29)
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 0.90 81.0 6.13e-01 93.8% 98.0%
1x9nA01 1.10.3260.10 Mainly Alpha › Orthogonal Bundle › DNA ligase i, domain 1 › DNA ligase, ATP-dependent, N-terminal domain 0.89 83.0 5.82e-01 100.0% 88.4%
3gdeA01 1.10.3260.10 Mainly Alpha › Orthogonal Bundle › DNA ligase i, domain 1 › DNA ligase, ATP-dependent, N-terminal domain 0.87 81.0 6.04e-01 100.0% 98.2%
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 5.66e-01 99.0% 98.6%
2ggfA00 1.25.40.180 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.64 48.0 4.29e-01 80.2% 86.9%
7p2yd01 1.10.520.20 Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › N-terminal domain of the delta subunit of the F1F0-ATP synthase 0.61 38.0 3.78e-01 76.0% 60.6%
4uf1A00 1.10.437.10 Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › Blc2-like 0.60 45.0 4.08e-01 89.6% 57.8%
3h20A04 1.10.1240.50 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › 0.60 41.0 4.27e-01 91.7% 77.5%
4hehA01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.59 47.0 5.02e-01 93.8% 100.0%
1sz9C00 1.25.40.90 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.57 50.0 4.49e-01 100.0% 90.0%
5ejrA01 1.25.40.530 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › MyTH4 domain 0.56 47.0 3.78e-01 93.8% 64.2%
4ccjA01 2.60.120.650 Mainly Beta › Sandwich › Jelly Rolls › Cupin 0.56 48.0 3.61e-01 93.8% 99.2%
1xl3C00 1.20.1280.80 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.56 45.0 4.65e-01 93.8% 93.4%
3w3uA01 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.55 48.0 2.80e-01 100.0% 12.8%
5haxA01 1.20.58.1780 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.55 47.0 3.59e-01 97.9% 67.5%
2qk1A01 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.54 47.0 3.62e-01 100.0% 56.5%
2vvyA01 1.10.437.20 Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › dsDNA poxvirus 0.54 43.0 3.87e-01 86.5% 64.2%
6wm2P02 1.25.40.150 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › V-type ATPase, subunit H, C-terminal domain 0.54 41.0 4.00e-01 87.5% 73.4%
2kjgA00 1.20.120.970 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.54 35.0 3.52e-01 75.0% 64.6%
5cwhA01 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.53 47.0 4.04e-01 100.0% 79.5%
4yvoA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.53 40.0 3.74e-01 85.4% 64.7%
4ap2B01 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.53 42.0 3.80e-01 86.5% 85.8%
8jpdG01 1.10.167.10 Mainly Alpha › Orthogonal Bundle › Regulator of G-protein Signalling 4; domain 2 › Regulator of G-protein Signalling 4, domain 2 0.53 38.0 3.34e-01 75.0% 51.7%
3zc4A01 1.20.120.1610 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.52 33.0 3.40e-01 72.9% 66.7%
3o4yA01 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.51 35.0 3.44e-01 72.9% 81.8%
3qsgA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.50 36.0 3.43e-01 75.0% 100.0%
4dloB02 1.25.40.610 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.50 40.0 3.79e-01 90.6% 71.8%
3bulA01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.50 39.0 4.07e-01 87.5% 93.1%
2af7D00 1.20.1290.10 Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like 0.50 42.0 3.93e-01 93.8% 90.1%
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 0.91 87.0 5.43e-01 100.0% 48.7%
3221597 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 0.90 82.0 6.20e-01 94.8% 97.5%
4035726 109.4.1.144 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Ints3_N 0.60 53.0 3.80e-01 100.0% 51.4%
3280169 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.58 42.0 4.11e-01 84.4% 67.3%
3682347 109.4.1.1125 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_TAF2_C 0.57 47.0 3.36e-01 89.6% 31.5%
4567932 109.4.1.170 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › CLASP_N 0.57 50.0 2.94e-01 100.0% 13.3%
3673033 604.1.1.61 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › DUF6857 0.56 44.0 3.67e-01 85.4% 77.7%
3268456 109.6.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Ras GEF › Ras GEF 0.56 45.0 3.89e-01 87.5% 56.8%
5002258 109.7.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Cytochrome c oxidase subunit E › Cytochrome c oxidase subunit E 0.56 39.0 4.20e-01 87.5% 88.7%
3435402 109.4.1.1273 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_3 0.55 49.0 4.04e-01 100.0% 62.2%
3910361 138.1.1.2 ↗ alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › Rep_fac_C 0.55 42.0 4.27e-01 92.7% 83.2%
2875223 138.1.1.0 ↗ alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain 0.55 42.0 4.28e-01 91.7% 84.0%
3708654 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.54 46.0 3.73e-01 95.8% 68.2%
3421182 109.4.1.603 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TAF1_subA 0.54 49.0 4.19e-01 99.0% 70.7%
3311601 109.4.1.1256 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3 0.54 47.0 3.22e-01 99.0% 31.7%
4224451 109.4.1.3082 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PF27498 0.53 47.0 3.48e-01 95.8% 40.4%
3628636 109.4.1.631 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › SRP72 0.52 46.0 3.34e-01 94.8% 37.7%
3246418 109.54.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › C-terminal tetramerization domain of Utp1/Utp21/Utp12/Utp13 › C-terminal tetramerization domain of Utp1/Utp21/Utp12/Utp13 0.51 44.0 4.09e-01 97.9% 92.0%
3299317 604.1.1.96 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Bap31 0.51 36.0 3.30e-01 72.9% 90.4%
D3 medium residues 54-161
PDB
Domain cluster: rep: DNA_ligase__YP_009506208__Trichoplusia_ni_granulovirus_LBIV-12__1916701__D77-175
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF04675.20 best DNA_ligase_A_N 77.1 2.80e-21 100.0% 61.5%
D4 medium residues 205-236_360-407
PDB
Domain cluster: rep: ON649702__UVF62572.1__X__00095__D231-262_382-434
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01068.27 best DNA_ligase_A_M 40.8 2.70e-10 65.0% 24.5%
D5 medium residues 237-359
PDB
Domain cluster: rep: DNA_ligase-like_protein__YP_009408099__Eptesipox_virus__1329402__D250-350
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01068.27 best DNA_ligase_A_M 131.8 3.70e-38 100.0% 62.3%