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DNA_methyltransferase

Euk-Vir

Lymphocystis_disease_virus_4

DNA_methyltransferase__YP_010087928__Lymphocystis_disease_virus_4__2704413

Identity

Accession:
YP_010087928 ↗
Protein ID:
DNA_methyltransferase
Kingdom:
euk

Quality

90.6 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Megaviricetes› Pimascovirales› Iridoviridae› Lymphocystivirus› Lymphocystis_disease_virus_4

TaxID: 2704413

Cluster

View cluster (29 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 2-227
PDB
Domain cluster: representative
CATH (48)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4ft4A02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.70 66.0 5.52e-01 98.2% 92.0%
1p2fA01 3.40.50.2300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Response regulator 0.70 37.0 5.09e-01 96.9% 97.5%
3pt9A02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.69 64.0 5.71e-01 96.9% 90.7%
4gx0B04 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.69 40.0 5.12e-01 78.3% 97.7%
3on5B02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.68 46.0 5.52e-01 100.0% 99.4%
1lsuA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.68 40.0 5.13e-01 73.9% 98.5%
3fwzA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.66 39.0 4.93e-01 73.5% 94.3%
1lssA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.65 38.0 4.95e-01 72.6% 99.2%
4tkzA00 3.40.50.510 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphotransferase system, mannose-type IIA component 0.65 33.0 4.16e-01 96.5% 81.5%
4ew6A01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.65 33.0 4.50e-01 90.7% 93.3%
3l9wA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.64 41.0 4.72e-01 79.2% 86.5%
2ggsA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.63 48.0 5.09e-01 94.7% 86.8%
1pdoA00 3.40.50.510 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphotransferase system, mannose-type IIA component 0.63 32.0 4.09e-01 96.9% 82.9%
3d7lA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.63 51.0 5.36e-01 96.0% 94.1%
3e9nA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.61 47.0 5.12e-01 97.3% 94.2%
4bluB00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.61 47.0 4.39e-01 79.2% 83.7%
1id1A00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.61 40.0 4.76e-01 94.2% 96.7%
3gemD00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.60 51.0 5.25e-01 96.0% 92.1%
2jfzB01 3.40.50.1860 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.59 30.0 3.81e-01 95.6% 80.8%
2d4aD01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.59 37.0 4.59e-01 70.4% 100.0%
5vyqA01 3.40.50.170 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Formyl transferase, N-terminal domain 0.58 41.0 4.58e-01 96.9% 91.0%
3oh8A02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.57 50.0 4.76e-01 92.0% 93.5%
2amfA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.57 37.0 4.42e-01 92.5% 98.0%
1u9jA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.56 51.0 4.95e-01 97.3% 87.7%
3m2pB00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.56 50.0 4.82e-01 93.8% 91.8%
7ztnA01 3.40.50.1110 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › SGNH hydrolase 0.56 50.0 4.53e-01 95.6% 100.0%
1gc5A01 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.56 50.0 4.24e-01 95.1% 91.7%
3kkjA01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.56 37.0 4.44e-01 95.6% 98.7%
1fjhA00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.56 50.0 4.98e-01 96.0% 90.7%
4xcvA02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.55 36.0 3.92e-01 89.4% 77.5%
2x9qB00 3.40.50.11710 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Cyclodipeptide synthase 0.55 41.0 4.18e-01 90.3% 76.6%
1eamA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.55 48.0 4.38e-01 93.4% 71.6%
6qmmA02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.55 43.0 4.36e-01 92.5% 82.6%
1reoA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.55 36.0 4.35e-01 95.6% 100.0%
2uyyA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.54 38.0 4.29e-01 93.8% 93.5%
3l6dA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.54 37.0 4.27e-01 92.5% 94.5%
2x5fA01 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.54 41.0 3.66e-01 79.2% 56.3%
4wjmA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.53 49.0 4.40e-01 98.7% 87.2%
7qccA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.53 38.0 4.12e-01 96.0% 85.9%
3rq1A02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.53 40.0 4.01e-01 79.2% 77.4%
3l8uA00 3.40.1280.10 Alpha Beta › 3-Layer(aba) Sandwich › Alpha/beta knot › SPOUT methyltransferase, trefoil knot domain 0.52 33.0 3.96e-01 96.9% 92.9%
3o0hB02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.52 27.0 3.61e-01 92.0% 94.0%
6wctD01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.52 32.0 3.93e-01 100.0% 93.9%
7n3yC01 3.60.10.10 Alpha Beta › 4-Layer Sandwich › Deoxyribonuclease I; Chain A › Endonuclease/exonuclease/phosphatase 0.52 46.0 3.91e-01 94.2% 83.9%
1hkuA02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.52 34.0 3.60e-01 89.4% 74.2%
1xdwA02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 35.0 3.70e-01 89.4% 77.2%
1dxyA02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 34.0 3.67e-01 89.4% 77.0%
3fbsB01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.50 40.0 4.32e-01 96.0% 98.4%
ECOD (26)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3184404 2003.1.5.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › DNA_methylase 0.78 73.0 5.75e-01 97.3% 97.4%
4588619 2003.1.5.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › DNA_methylase 0.78 72.0 5.65e-01 96.5% 99.8%
3295997 2003.1.5.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › DNA_methylase 0.77 73.0 5.62e-01 98.7% 96.1%
3465494 2003.1.5.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › DNA_methylase 0.77 71.0 5.38e-01 97.8% 90.8%
3620163 2003.1.5.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › DNA_methylase 0.71 65.0 5.54e-01 95.6% 96.6%
4453077 2003.1.10.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › PreATP-grasp domain 0.69 30.0 4.31e-01 95.1% 84.5%
4988360 2003.1.1.28 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › TrkA_N 0.66 39.0 5.03e-01 74.3% 100.0%
3696698 2007.1.3.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › CheY-like 0.64 35.0 4.62e-01 95.6% 95.9%
4960172 2003.1.5.81 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_25 0.64 45.0 4.69e-01 97.3% 76.2%
3953074 2003.1.5.81 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_25 0.64 43.0 5.14e-01 97.3% 96.9%
None — 0.63 51.0 5.38e-01 96.0% 95.0%
3971071 2003.1.1.69 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › adh_short_C2 0.62 51.0 5.31e-01 95.6% 91.8%
3945390 2010.1.1.3 ↗ a/b three-layered sandwiches › EDD domain › EDD domain › EDD domain › EIIA-man 0.59 31.0 3.91e-01 97.3% 82.2%
3965671 2003.1.2.24 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › Pyr_redox_2 0.58 37.0 4.36e-01 95.6% 92.3%
5025271 2003.1.1.37 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › 2-Hacid_dh_C 0.55 34.0 3.80e-01 79.2% 76.1%
3259700 2003.1.1.188 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › Methyltransf_12, KR 0.55 50.0 3.21e-01 96.0% 22.5%
4938094 2003.1.1.20 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › Epimerase 0.55 49.0 4.70e-01 93.8% 99.2%
3450582 2005.1.1.0 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains 0.54 28.0 3.64e-01 93.4% 85.4%
4016170 2003.1.5.176 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › BMT5-like 0.54 49.0 4.70e-01 95.6% 95.4%
3589880 2010.1.1.3 ↗ a/b three-layered sandwiches › EDD domain › EDD domain › EDD domain › EIIA-man 0.54 32.0 3.93e-01 76.1% 94.8%
3587536 2010.1.1.3 ↗ a/b three-layered sandwiches › EDD domain › EDD domain › EDD domain › EIIA-man 0.53 31.0 3.89e-01 78.3% 94.8%
5028665 2003.1.5.66 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_11 0.53 41.0 4.20e-01 96.0% 82.2%
1837559 7577.1.1.1 ↗ a/b three-layered sandwiches › PLP-dependent transferases › PLP-dependent transferases › PLP-dependent transferases › Aminotran_1_2 0.53 41.0 3.78e-01 79.2% 65.4%
3633072 2003.1.5.81 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_25 0.52 45.0 4.03e-01 88.9% 75.8%
4987814 2003.1.5.66 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_11 0.52 41.0 4.26e-01 97.3% 85.8%
3559665 213.1.1.6 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › ODC_AZ 0.51 29.0 3.79e-01 96.5% 96.9%