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DNA_methylase_N-4_N-6

Euk-Vir

Pandoravirus_inopinatum

DNA_methylase_N-4_N-6__YP_009119985__Pandoravirus_inopinatum__1605721

Identity

Accession:
YP_009119985 ↗
Protein ID:
DNA_methylase_N-4_N-6
Kingdom:
euk

Quality

73.9 mean pLDDT

Taxonomy

Pandoravirus› Pandoravirus_inopinatum

TaxID: 1605721

Cluster

View cluster (7 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 94-185
PDB
Domain cluster: representative
CATH (35)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
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 0.72 55.0 5.40e-01 81.5% 84.0%
2oebA00 1.10.520.30 Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › AF1862-like domain 0.69 60.0 5.08e-01 95.7% 89.5%
2ra1A03 1.20.58.770 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.63 35.0 4.07e-01 94.6% 77.8%
6ygiB01 1.10.4090.10 Mainly Alpha › Orthogonal Bundle › Hepatitis B viral capsid (hbcag) fold › Viral capsid, core domain supefamily, Hepatitis B virus 0.62 36.0 3.10e-01 91.3% 34.9%
6zhiB02 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.61 37.0 3.94e-01 94.6% 67.5%
2a0bA00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.61 52.0 4.88e-01 97.8% 94.9%
1nklA00 1.10.225.10 Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like 0.59 46.0 4.88e-01 89.1% 100.0%
1j8yF01 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.58 43.0 4.43e-01 78.3% 97.7%
2m3aA00 1.10.10.1900 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Knl-2 Myb-like DNA-binding domain-like 0.58 37.0 4.12e-01 89.1% 86.6%
2o36A01 1.20.1050.40 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › Endopeptidase. Chain P; domain 1 0.58 41.0 3.68e-01 97.8% 53.1%
1v1gA00 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.58 44.0 3.55e-01 82.6% 79.3%
3ls1A00 1.20.120.290 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Oxygen-evolving enhancer protein 3 (PsbQ), four-helix up-down bundle 0.58 47.0 4.25e-01 91.3% 79.7%
3e3vA03 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 0.58 35.0 4.16e-01 72.8% 100.0%
3c18A02 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.57 47.0 4.33e-01 89.1% 91.5%
1yozA00 1.10.3200.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af0941 › AF0941-like 0.57 45.0 4.16e-01 100.0% 67.3%
3k3uA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.57 42.0 3.70e-01 78.3% 68.6%
5iduA01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.56 45.0 4.17e-01 88.0% 75.0%
1c9bA01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.56 34.0 3.43e-01 78.3% 58.8%
6yz2A01 1.20.120.350 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels. Chain C 0.55 45.0 4.20e-01 91.3% 87.5%
1f5qB02 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.55 39.0 3.46e-01 75.0% 60.9%
1sr2A00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.54 45.0 4.24e-01 93.5% 80.2%
3dkaB01 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.54 46.0 4.08e-01 93.5% 79.3%
3rvyA01 1.20.120.350 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Voltage-gated potassium channels. Chain C 0.54 43.0 4.07e-01 90.2% 95.6%
1aj5A00 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.53 48.0 3.89e-01 100.0% 70.5%
6ynwH01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.53 33.0 3.61e-01 92.4% 78.4%
3r72A00 1.10.238.20 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain 0.52 39.0 3.57e-01 79.3% 90.2%
2yguC00 1.10.238.190 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › 0.52 40.0 3.71e-01 83.7% 68.6%
3rlfG01 1.10.3720.10 Mainly Alpha › Orthogonal Bundle › MetI-like fold › MetI-like 0.52 44.0 3.19e-01 94.6% 51.6%
4ioeA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.51 34.0 3.51e-01 93.5% 71.3%
3pm8B01 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.51 37.0 3.88e-01 91.3% 86.9%
7dfeA01 1.10.274.60 Mainly Alpha › Orthogonal Bundle › Enzyme I; Chain A, domain 2 › Spidroin, repetitive domain 0.51 38.0 3.44e-01 79.3% 69.3%
1f7uA02 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.50 35.0 3.26e-01 95.7% 54.4%
3cz1A00 1.10.238.20 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › Pheromone/general odorant binding protein domain 0.50 35.0 3.34e-01 75.0% 68.4%
4ar9A02 1.10.390.20 Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › 0.50 43.0 3.84e-01 100.0% 78.2%
2f48A03 1.10.10.480 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Phosphofructokinase; domain 3 0.50 37.0 3.97e-01 78.3% 98.7%
ECOD (28)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3675734 109.3.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat 0.71 37.0 3.65e-01 95.7% 46.0%
4957771 5069.1.3.137 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Fumarate reductase respiratory complex transmembrane subunits › DUF7521 0.68 37.0 3.77e-01 92.4% 53.3%
4985507 604.10.1.0 ↗ alpha bundles › Spectrin repeat-like › Enzyme IIa from lactose specific PTS, IIa-lac › Enzyme IIa from lactose specific PTS, IIa-lac 0.66 41.0 4.13e-01 97.8% 62.2%
3728445 551.1.1.0 ↗ alpha arrays › Hsp90 co-chaperone CDC37 middle domain › Hsp90 co-chaperone CDC37 middle domain › Hsp90 co-chaperone CDC37 middle domain 0.62 52.0 4.59e-01 90.2% 83.7%
4340169 601.3.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain › Hpt 0.62 54.0 4.93e-01 96.7% 91.1%
4554328 604.3.1.0 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.61 39.0 4.01e-01 94.6% 67.0%
3704699 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.58 45.0 4.51e-01 96.7% 78.9%
3317539 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.58 36.0 3.39e-01 93.5% 48.7%
4105784 192.7.1.3 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Phe_tRNA-synt_N 0.58 44.0 4.26e-01 97.8% 72.0%
3982476 601.3.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine-containing phosphotransfer domain, HPT domain › Histidine-containing phosphotransfer domain, HPT domain › Hpt 0.57 49.0 4.54e-01 95.7% 90.0%
3792321 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.56 38.0 3.99e-01 72.8% 75.3%
3705963 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.56 35.0 3.37e-01 91.3% 54.3%
2543635 108.2.1.1 ↗ alpha arrays › EF-hand › Insect pheromone/odorant-binding proteins › Insect pheromone/odorant-binding proteins › PBP_GOBP 0.56 43.0 3.99e-01 82.6% 94.1%
4467738 622.1.1.1 ↗ alpha bundles › YvfG-like › HSC20 (HSCB), C-terminal oligomerisation domain › HSC20 (HSCB), C-terminal oligomerisation domain › HSCB_C 0.55 40.0 4.12e-01 96.7% 80.0%
5052411 604.5.1.0 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) 0.54 42.0 4.11e-01 97.8% 76.0%
3599224 610.1.1.0 ↗ alpha arrays › ERP29 C domain-like › ERP29 C domain-like › ERP29 C domain-like 0.54 41.0 4.13e-01 89.1% 82.1%
4004087 108.1.1.179 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_5, EF-hand_8, EF-hand_FSTL1 0.54 39.0 3.51e-01 77.2% 67.4%
4104241 148.1.3.327 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › CCD48 0.54 32.0 3.24e-01 87.0% 55.8%
3989810 3291.1.1.5 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Relaxase_C 0.53 39.0 3.91e-01 92.4% 74.7%
3934748 108.1.1.30 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_8 0.53 41.0 3.67e-01 85.9% 92.6%
170038 132.2.1.1 ↗ alpha bundles › ACP-like › Colicin E immunity proteins › Colicin E immunity proteins › Colicin_Pyocin 0.52 40.0 4.00e-01 83.7% 90.3%
3225589 108.1.1.26 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_5 0.52 37.0 3.90e-01 75.0% 82.4%
3581248 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.52 36.0 3.73e-01 79.3% 78.8%
4335728 192.7.1.3 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Phe_tRNA-synt_N 0.51 39.0 3.75e-01 98.9% 70.5%
3873685 601.24.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) › FKBP12-rapamycin-binding domain of FKBP-rapamycin-associated protein (FRAP) 0.51 43.0 3.94e-01 95.7% 98.4%
3257188 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.51 40.0 3.59e-01 97.8% 60.8%
3832769 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.51 39.0 3.33e-01 96.7% 49.7%
3992517 109.4.1.391 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › UNC80_C 0.51 41.0 3.09e-01 91.3% 78.8%
D2 medium residues 38-93_187-218
PDB
Domain cluster: rep: Methyltransferase_incomplete_domain_containing_protein__YP_009483250__Pandoravirus_quercus__2107709__D39-93_184-204
D3 medium residues 219-386
PDB
Domain cluster: representative
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3e23A00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.57 41.0 3.92e-01 73.2% 96.5%
4m3sA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.56 40.0 4.15e-01 72.6% 93.1%
2i6gB00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.54 38.0 3.65e-01 72.6% 69.8%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4966689 2003.1.5.12 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › N6_N4_Mtase 0.82 57.0 4.27e-01 78.0% 31.3%
169085 2003.1.5.66 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_11 0.57 41.0 3.90e-01 72.6% 96.4%
4976892 2003.1.5.81 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_25 0.57 42.0 3.91e-01 76.2% 75.0%
4665923 3008.1.1.2 ↗ a+b three layers › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › A subdomain in the anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › DUF5915 0.53 25.0 3.36e-01 79.2% 83.3%
None — 0.51 30.0 3.37e-01 72.6% 72.6%