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restriction_endonuclease

Euk-Vir

Noumeavirus

restriction_endonuclease__YP_009345354__Noumeavirus__1955558

Identity

Accession:
YP_009345354 ↗
Protein ID:
restriction_endonuclease
Kingdom:
euk

Quality

78.3 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Megaviricetes› Pimascovirales› Marseilleviridae› Marseillevirus› Noumeavirus

TaxID: 1955558

Cluster

View cluster (37 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 medium residues 13-113
PDB
Domain cluster: rep: SRR1747018_scaffold_15_prodigal-single.1__X__X__00405__D414-500
D2 medium residues 114-171
PDB
Domain cluster: rep: restriction_endonuclease__YP_009345354__Noumeavirus__1955558__D260-319
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF14311.13 best DUF4379 32.8 8.70e-08 91.4% 80.4%
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5jzxD02 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.56 39.0 2.95e-01 72.4% 61.6%
2iz4A02 2.20.25.590 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.53 31.0 3.57e-01 82.8% 76.2%
1fsuA01 3.40.720.10 Alpha Beta › 3-Layer(aba) Sandwich › Alkaline Phosphatase, subunit A › Alkaline Phosphatase, subunit A 0.53 41.0 2.62e-01 91.4% 89.2%
3aa0B01 1.20.58.570 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › F-actin capping protein, alpha/beta subunit, N-terminal domain 0.52 38.0 3.34e-01 75.9% 62.5%
4ljiB00 1.10.760.10 Mainly Alpha › Orthogonal Bundle › Cytochrome Bc1 Complex; Chain D, domain 2 › Cytochrome c-like domain 0.52 36.0 2.80e-01 72.4% 81.7%
5yvxA00 3.30.40.100 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › 0.52 36.0 3.64e-01 75.9% 76.7%
1uxyA03 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.51 37.0 2.89e-01 81.0% 60.0%
6rwcA02 2.20.25.590 Mainly Beta › Single Sheet › N-terminal domain of TfIIb › 0.51 29.0 3.34e-01 82.8% 82.1%
7uqyB01 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.50 40.0 2.92e-01 100.0% 88.8%
ECOD (11)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3605531 375.1.1.77 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › DUF4379 0.75 61.0 5.33e-01 87.9% 61.9%
3598807 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.73 59.0 5.60e-01 87.9% 73.9%
3712524 375.1.1.77 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › DUF4379 0.73 59.0 6.03e-01 87.9% 92.7%
3592370 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.72 65.0 5.04e-01 100.0% 84.2%
3447963 375.3.1.0 ↗ few secondary structure elements › Rubredoxin-like › CSL zinc finger › CSL zinc finger 0.67 42.0 4.11e-01 70.7% 56.9%
4465307 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.63 37.0 3.89e-01 84.5% 64.0%
4978678 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.62 37.0 3.85e-01 74.1% 61.8%
4474017 217.1.1.2 ↗ a+b complex topology › FAD-binding domain-like › FAD-binding domain › FAD-binding domain › FAD_binding_4 0.56 38.0 2.73e-01 72.4% 72.6%
3989651 4.11.1.2 ↗ beta barrels › SH3 › LexA/Signal peptidase › LexA/Signal peptidase › Peptidase_S26 0.53 41.0 2.95e-01 89.7% 74.4%
3988057 3227.1.1.1 ↗ alpha complex topology › phosphorylation-coupled saccharide transporter ChbC › phosphorylation-coupled saccharide transporter ChbC › phosphorylation-coupled saccharide transporter ChbC › PTS_EIIC 0.51 41.0 2.56e-01 98.3% 44.7%
3560555 389.1.1.36 ↗ few secondary structure elements › EGF-like › EGF-related › EGF/Laminin › Ldl_recept_a 0.51 30.0 3.33e-01 84.5% 80.0%
D3 medium residues 172-259
PDB
Domain cluster: rep: SRR1747018_scaffold_15_prodigal-single.1__X__X__00405__D414-500
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF14311.13 best DUF4379 43.7 3.40e-11 60.2% 91.1%
D4 medium residues 260-319
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF14311.13 best DUF4379 36.8 4.90e-09 90.0% 94.6%
CATH (23)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4bwxA03 1.10.287.3700 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.60 45.0 4.14e-01 80.0% 77.5%
1igqB00 2.30.30.150 Mainly Beta › Roll › SH3 type barrels. › KorB, C-terminal domain 0.59 41.0 4.20e-01 75.0% 75.4%
1g5hB02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.59 43.0 3.59e-01 78.3% 87.9%
3kk4A01 1.10.3990.20 Mainly Alpha › Orthogonal Bundle › Ribbon-helix-helix fold › protein bp1543 0.58 39.0 3.22e-01 70.0% 56.0%
7wa9A01 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.57 46.0 3.67e-01 96.7% 66.7%
3rauA00 1.25.40.280 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › alix/aip1 like domains 0.56 42.0 2.66e-01 83.3% 43.9%
3zuaA01 3.90.70.10 Alpha Beta › Alpha-Beta Complex › Cathepsin B; Chain A › Cysteine proteinases 0.56 37.0 2.94e-01 78.3% 32.1%
2d9tA01 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.55 39.0 4.30e-01 75.0% 95.9%
3wt0A02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.55 40.0 2.99e-01 78.3% 36.3%
6ieoA03 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.55 37.0 3.26e-01 70.0% 85.1%
4xr7F02 1.10.287.3700 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.54 40.0 3.54e-01 80.0% 68.9%
2do3A01 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.54 37.0 3.99e-01 75.0% 86.3%
1adjB02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.53 41.0 3.64e-01 90.0% 96.8%
1nj1A02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.52 41.0 3.52e-01 88.3% 93.3%
4c5eC02 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.52 35.0 3.05e-01 70.0% 71.9%
1xjkA00 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.52 38.0 2.20e-01 80.0% 10.9%
7co7D03 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.51 34.0 3.07e-01 70.0% 93.6%
4fw1A02 2.30.30.10 Mainly Beta › Roll › SH3 type barrels. › Integrase, C-terminal domain superfamily, retroviral 0.51 36.0 3.73e-01 73.3% 81.5%
1te0A03 2.30.42.10 Mainly Beta › Roll › Pdz3 Domain › PDZ domain 0.51 35.0 3.05e-01 71.7% 89.0%
7u32F02 2.30.30.10 Mainly Beta › Roll › SH3 type barrels. › Integrase, C-terminal domain superfamily, retroviral 0.51 36.0 3.82e-01 75.0% 92.2%
5e3iA02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.51 39.0 3.44e-01 90.0% 97.0%
2i4lB02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.50 37.0 3.20e-01 80.0% 89.1%
5xilA02 3.40.50.800 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Anticodon-binding domain 0.50 40.0 3.23e-01 91.7% 63.3%
ECOD (18)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3592370 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.86 74.0 5.80e-01 93.3% 51.7%
3598807 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.85 71.0 6.75e-01 90.0% 85.5%
3605531 375.1.1.77 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › DUF4379 0.84 72.0 6.34e-01 91.7% 72.6%
3712524 375.1.1.77 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › DUF4379 0.83 62.0 6.46e-01 80.0% 94.5%
3739884 1016.1.1.1 ↗ alpha arrays › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › Pan3_PK 0.61 45.0 3.54e-01 80.0% 69.8%
4778018 1016.1.1.1 ↗ alpha arrays › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › Pan3_PK 0.60 44.0 3.99e-01 78.3% 75.6%
2321219 1016.1.1.1 ↗ alpha arrays › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › Pan3_PK 0.60 44.0 3.45e-01 80.0% 58.2%
3514631 1016.1.1.1 ↗ alpha arrays › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › Dimerization domain in caprin-1 and PAN3 › Pan3_PK 0.60 45.0 3.57e-01 80.0% 75.8%
4940298 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.58 42.0 3.76e-01 80.0% 97.8%
2561794 316.1.1.0 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.55 40.0 2.95e-01 78.3% 64.3%
4994502 7.1.1.0 ↗ beta barrels › PDZ domain › PDZ domain › PDZ domain 0.55 40.0 3.52e-01 78.3% 93.7%
3627688 4.1.1.319 ↗ beta barrels › SH3 › SH3 › SH3 › SH3_Hsr9 0.55 40.0 3.00e-01 78.3% 85.3%
3398093 4.1.1.43 ↗ beta barrels › SH3 › SH3 › SH3 › SMN_Tudor 0.53 36.0 3.65e-01 70.0% 71.7%
3579075 380.1.1.13 ↗ few secondary structure elements › Kringle-like › Kringle-like › Kringle-like › PF25866 0.53 36.0 3.15e-01 71.7% 63.8%
3680858 192.2.1.0 ↗ alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.53 39.0 2.86e-01 80.0% 47.9%
4297095 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.52 41.0 3.49e-01 90.0% 89.5%
4946192 2004.1.1.1197 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › TGS 0.52 41.0 3.10e-01 96.7% 85.0%
4375036 7502.1.1.1 ↗ a/b three-layered sandwiches › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › Anticodon-binding domain of Class II aaRS › HGTP_anticodon 0.51 40.0 3.48e-01 88.3% 92.0%
D5 medium residues 324-378
PDB
Domain cluster: rep: restriction_endonuclease__YP_009345354__Noumeavirus__1955558__D260-319