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Numod4_NHN_endonuclease

Euk-Vir

Acanthamoeba_polyphaga_moumouvirus

Numod4_NHN_endonuclease__YP_007354561__Acanthamoeba_polyphaga_moumouvirus__1269028

Identity

Accession:
YP_007354561 ↗
Protein ID:
Numod4_NHN_endonuclease
Kingdom:
euk

Quality

82.5 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Megaviricetes› Imitervirales› Mimiviridae› Moumouvirus› Acanthamoeba_polyphaga_moumouvirus

TaxID: 1269028

Cluster

View cluster (21 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 16-111
PDB
Domain cluster: rep: CG10_big_fil_rev_8_21_14_0-10_scaffold_17_prodigal-single.1__X__X__00096__D70-143
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF13392.13 best HNH_3 45.3 7.20e-12 45.8% 89.1%
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1u3eM01 3.90.75.20 Alpha Beta › Alpha-Beta Complex › Homing Intron 3 (I-Ppo) Encoded Endonuclease; Chain A › 0.82 59.0 5.67e-01 74.0% 89.6%
1a73A00 3.90.75.10 Alpha Beta › Alpha-Beta Complex › Homing Intron 3 (I-Ppo) Encoded Endonuclease; Chain A › Homing Intron 3 (I-ppo) Encoded Endonuclease; Chain A 0.59 52.0 4.33e-01 95.8% 61.7%
3u4zA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.56 37.0 3.56e-01 94.8% 58.7%
8aa9A01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.50 35.0 3.39e-01 93.8% 62.3%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3539740 378.1.1.19 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › HNH_3 0.86 78.0 7.04e-01 94.8% 82.4%
3586841 378.1.1.7 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › NUMOD4,HNH_3 0.79 58.0 5.40e-01 76.0% 80.0%
89916 378.1.1.0 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases 0.59 52.0 4.34e-01 95.8% 61.7%
8233 378.1.1.6 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › zf-His_Me_endon 0.59 52.0 4.33e-01 95.8% 61.7%
4618920 2.1.1.127 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › tRNA_anti_2 0.57 36.0 3.30e-01 89.6% 48.5%
3695527 378.1.1.6 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › zf-His_Me_endon 0.56 46.0 4.28e-01 100.0% 71.7%
185780 378.1.1.2 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases › HNH 0.55 38.0 3.84e-01 82.3% 70.1%
4950121 211.1.1.5 ↗ a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase_2 0.51 25.0 3.05e-01 78.1% 73.3%
4546532 2.1.1.15 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › tRNA_anti-codon 0.50 33.0 3.26e-01 92.7% 61.9%
D2 medium residues 112-177
PDB
Domain cluster: rep: MW960032.1__QWY83295.1__X__00089__D170-241
CATH (36)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2j3wC00 3.30.450.70 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.67 47.0 3.77e-01 84.8% 36.3%
3jtzA00 3.30.160.390 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Integrase, DNA-binding domain 0.67 48.0 4.59e-01 77.3% 100.0%
1z1bA01 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.66 46.0 4.82e-01 75.8% 86.0%
6yiiA01 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.64 47.0 3.20e-01 77.3% 71.4%
1mgpA02 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.64 57.0 4.65e-01 100.0% 70.2%
3nyiA02 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.60 52.0 4.15e-01 98.5% 69.3%
1h10A00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.59 43.0 3.66e-01 86.4% 45.3%
7oufB01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.59 50.0 3.96e-01 100.0% 47.0%
3zl8A02 3.40.1190.10 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Mur-like, catalytic domain 0.58 44.0 3.12e-01 83.3% 34.1%
6f95A01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.58 48.0 3.80e-01 95.5% 86.5%
7t8tA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.58 40.0 3.27e-01 72.7% 49.6%
3io5A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.57 45.0 3.07e-01 89.4% 91.9%
2l33A00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.57 43.0 3.95e-01 84.8% 60.4%
2yt4A03 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.57 44.0 3.84e-01 87.9% 54.8%
5eoxB03 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.56 48.0 3.97e-01 100.0% 93.0%
4c23B01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.56 47.0 3.32e-01 100.0% 93.6%
4cllA01 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.55 48.0 3.42e-01 100.0% 47.6%
3picA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.55 47.0 3.01e-01 100.0% 34.3%
2memA00 3.90.1150.190 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › SLED domain 0.54 45.0 3.87e-01 100.0% 79.0%
2r16A00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.53 46.0 3.45e-01 100.0% 77.7%
4bq6F00 3.40.1000.10 Alpha Beta › 3-Layer(aba) Sandwich › Protein Transport Mog1p; Chain A › Mog1/PsbP, alpha/beta/alpha sandwich 0.53 39.0 3.14e-01 81.8% 46.3%
1azpA00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.53 33.0 3.31e-01 87.9% 60.6%
5l10B00 3.30.450.80 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Transcription factor LuxR-like, autoinducer-binding domain 0.53 37.0 2.88e-01 77.3% 44.1%
4e5xG00 2.60.40.3530 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 45.0 3.97e-01 98.5% 72.7%
2bmbA02 3.20.20.20 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Dihydropteroate synthase-like 0.52 41.0 2.65e-01 86.4% 100.0%
1efpB00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.52 46.0 3.13e-01 100.0% 56.1%
4m7xA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.52 42.0 3.86e-01 98.5% 67.0%
5w7zA01 3.10.150.10 Alpha Beta › Roll › DNA Polymerase III; Chain A, domain 2 › DNA Polymerase III, subunit A, domain 2 0.52 40.0 3.38e-01 100.0% 49.6%
1cnzA00 3.40.718.10 Alpha Beta › 3-Layer(aba) Sandwich › Isopropylmalate Dehydrogenase › Isopropylmalate Dehydrogenase 0.51 44.0 2.83e-01 100.0% 44.4%
1bf3A01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.51 41.0 2.86e-01 89.4% 82.5%
3nm6B00 3.40.50.1580 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleoside phosphorylase domain 0.51 43.0 3.06e-01 100.0% 84.7%
2e87A02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 40.0 2.94e-01 89.4% 88.2%
1o8vA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.51 41.0 3.37e-01 92.4% 91.0%
3c4sA00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.50 37.0 3.87e-01 83.3% 91.2%
2gzaA01 3.30.450.90 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.50 33.0 2.83e-01 75.8% 41.7%
4l2iB00 3.40.50.620 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HUPs 0.50 43.0 2.95e-01 100.0% 50.6%
ECOD (51)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3827127 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.90 72.0 6.27e-01 84.8% 61.1%
3331331 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.88 72.0 6.14e-01 86.4% 57.0%
3661849 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.87 72.0 7.35e-01 86.4% 92.1%
3334492 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.86 66.0 6.12e-01 86.4% 66.3%
3664743 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.85 70.0 6.09e-01 87.9% 67.4%
3468885 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.84 73.0 6.76e-01 92.4% 88.7%
3164102 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.84 55.0 6.50e-01 83.3% 100.0%
3979711 252.2.1.6 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › Arm-DNA-bind_2 0.76 52.0 5.27e-01 71.2% 78.5%
4028013 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.73 53.0 5.14e-01 77.3% 78.7%
4027686 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.68 46.0 4.93e-01 71.2% 100.0%
3633647 896.1.1.0 ↗ a+b two layers › SRP9/14-like › Signal recognition particle alu RNA binding heterodimer SRP9/14-related › Signal recognition particle alu RNA binding heterodimer SRP9/14-related 0.67 43.0 4.35e-01 100.0% 66.2%
3728783 223.2.1.15 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Longin 0.66 49.0 3.86e-01 80.3% 70.0%
4027687 330.3.1.0 ↗ a+b two layers › dsRBD-like › Peptidyl-tRNA hydrolase domain-like › Peptidyl-tRNA hydrolase domain-like 0.65 47.0 5.03e-01 77.3% 100.0%
3514660 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.65 48.0 4.37e-01 87.9% 58.9%
3750640 220.1.1.38 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › UCH_N 0.65 48.0 4.10e-01 90.9% 48.2%
4029445 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.64 44.0 4.68e-01 72.7% 98.2%
4030681 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.64 45.0 4.56e-01 74.2% 84.6%
1937542 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.64 57.0 4.58e-01 100.0% 72.2%
3743110 220.1.1.19 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Rttp106-like_middle 0.63 43.0 3.68e-01 92.4% 44.8%
4944466 301.13.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain 0.62 54.0 4.38e-01 97.0% 72.0%
4944129 301.13.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain 0.61 53.0 4.24e-01 97.0% 70.0%
3991383 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.61 47.0 4.29e-01 84.8% 62.2%
3250597 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.60 40.0 3.35e-01 71.2% 40.9%
4030197 2004.1.1.250 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Kinesin,Microtub_bd 0.60 48.0 2.95e-01 90.9% 37.4%
3702572 2004.1.1.250 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Kinesin,Microtub_bd 0.59 48.0 3.09e-01 92.4% 36.0%
4024768 330.3.1.7 ↗ a+b two layers › dsRBD-like › Peptidyl-tRNA hydrolase domain-like › Peptidyl-tRNA hydrolase domain-like › AP2 0.59 43.0 4.61e-01 87.9% 96.4%
3230359 207.1.1.66 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › DUF3557 0.58 48.0 3.22e-01 97.0% 25.8%
4944239 301.13.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain 0.58 51.0 4.13e-01 100.0% 73.1%
3888556 220.1.1.48 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › Jak1_Phl 0.57 44.0 3.46e-01 97.0% 37.4%
4681706 1046.1.1.1 ↗ alpha bundles › Lipoprotein signal peptidase › Lipoprotein signal peptidase › Lipoprotein signal peptidase › Peptidase_A8 0.56 39.0 2.96e-01 74.2% 85.4%
3595871 511.1.1.0 ↗ beta sandwiches › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain › Heat shock protein 70kD (HSP70), peptide-binding domain 0.55 39.0 2.54e-01 75.8% 37.5%
1731428 2484.1.1.10 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › TsaD 0.55 46.0 4.04e-01 97.0% 74.5%
4249934 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.55 46.0 3.85e-01 97.0% 65.8%
3931122 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.55 36.0 3.24e-01 72.7% 47.4%
4068244 2484.1.1.49 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Hydant_A_N 0.54 46.0 3.66e-01 100.0% 60.7%
5081878 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.54 46.0 2.93e-01 97.0% 96.9%
3630575 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.54 47.0 3.17e-01 100.0% 29.8%
5015520 71.1.1.0 ↗ beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB 0.54 39.0 2.76e-01 78.8% 91.0%
3596544 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.53 45.0 3.93e-01 97.0% 91.4%
5000651 2484.1.1.34 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DNA_pol_B_exo1 0.53 45.0 2.84e-01 98.5% 31.8%
3474254 316.1.1.0 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase 0.53 38.0 3.01e-01 86.4% 37.0%
3213706 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.53 44.0 3.20e-01 100.0% 35.0%
220332 11.1.1.71 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Adeno_GP19K 0.52 45.0 3.97e-01 98.5% 72.7%
None — 0.52 44.0 2.54e-01 100.0% 33.9%
3066252 4032.1.1.1 ↗ beta complex topology › barrel domains in phase 1 flagellin › barrel domains in phase 1 flagellin › barrel domains in phase 1 flagellin › Flagellin_IN 0.52 40.0 3.56e-01 87.9% 56.9%
3781831 223.2.1.28 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Afi1 0.52 44.0 3.31e-01 100.0% 72.2%
4227866 2003.1.2.5 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FMO-like 0.51 41.0 2.72e-01 92.4% 29.4%
3791314 220.1.1.2 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › WH1 0.51 40.0 3.24e-01 87.9% 71.9%
3462090 5.1.3.144 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › b-prop_At3g26010-like 0.51 43.0 2.74e-01 97.0% 47.8%
4966955 330.7.1.2 ↗ a+b two layers › dsRBD-like › PI-Pfui intein middle domain › PI-Pfui intein middle domain › HicA_toxin 0.50 38.0 3.76e-01 84.8% 90.0%
4959982 3110.1.1.0 ↗ a/b three-layered sandwiches › STT3/PglB/AglB core domain › STT3/PglB/AglB core domain › STT3/PglB/AglB core domain 0.50 39.0 2.83e-01 87.9% 95.6%