←Back to structures

HNH_endonuclease

Euk-Vir

Acanthamoeba_polyphaga_moumouvirus

HNH_endonuclease__YP_007354355__Acanthamoeba_polyphaga_moumouvirus__1269028

Identity

Accession:
YP_007354355 ↗
Protein ID:
HNH_endonuclease
Kingdom:
euk

Quality

83.4 mean pLDDT

Taxonomy

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

TaxID: 1269028

Cluster

View cluster (6 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 7-105
PDB
Domain cluster: rep: OP056089.1__UYD72102.1__X__00002__D5-102
Pfam (2)
AccessionNameScoreE-valueQ covHMM cov
PF13392.13 best HNH_3 35.4 8.70e-09 46.5% 93.5%
PF07463.17 NUMOD4 28.5 2.00e-06 41.4% 93.9%
D2 high residues 181-282
PDB
Domain cluster: rep: OP056089.1__UYD72102.1__X__00002__D5-102
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF13392.13 best HNH_3 25.4 1.20e-05 47.1% 93.5%
D3 high residues 285-339
PDB
Domain cluster: rep: IMGVR_UViG_3300021426_000003-3300021426-Ga0224482_10000072181__D164-213
CATH (22)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1u3eM02 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 0.81 69.0 6.40e-01 100.0% 75.0%
1t3yA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.62 42.0 3.20e-01 98.2% 29.8%
4j3vA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 44.0 3.54e-01 100.0% 40.0%
4d7sA02 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.61 44.0 3.30e-01 100.0% 31.5%
6ea2A04 2.60.40.1840 Mainly Beta › Sandwich › Immunoglobulin-like › Aminopeptidase N, middle-beta domain 0.61 44.0 3.66e-01 100.0% 44.8%
2j6lA01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.58 39.0 2.49e-01 70.9% 64.3%
4jysB00 3.10.50.40 Alpha Beta › Roll › Chitinase A; domain 3 › 0.58 49.0 3.98e-01 100.0% 66.7%
4dipH00 3.10.50.40 Alpha Beta › Roll › Chitinase A; domain 3 › 0.57 49.0 3.90e-01 100.0% 68.1%
7kmfJ01 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 0.57 40.0 2.91e-01 98.2% 25.9%
4f3xA01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.57 39.0 2.48e-01 70.9% 66.8%
3qrxA02 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.57 42.0 3.99e-01 81.8% 83.8%
3eipA00 3.10.50.20 Alpha Beta › Roll › Chitinase A; domain 3 › Cloacin immunity protein 0.55 44.0 4.00e-01 98.2% 94.0%
5jzxD02 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.54 36.0 2.75e-01 100.0% 26.0%
3h7lA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 46.0 3.80e-01 98.2% 54.8%
1bu6O01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.53 47.0 3.01e-01 100.0% 32.7%
2ex2A01 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.53 39.0 2.62e-01 81.8% 64.9%
3x17A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.53 43.0 3.51e-01 90.9% 61.8%
1p6oA00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.53 46.0 3.35e-01 100.0% 67.9%
3gqqA00 2.70.50.40 Mainly Beta › Distorted Sandwich › Coagulation Factor XIII; Chain A, domain 1 › GMP phosphodiesterase, delta subunit 0.51 39.0 2.95e-01 92.7% 73.1%
2wanA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 40.0 3.32e-01 89.1% 70.6%
3d33A00 2.60.40.3080 Mainly Beta › Sandwich › Immunoglobulin-like › 0.50 40.0 3.45e-01 90.9% 61.7%
2nmlA00 3.30.2260.10 Alpha Beta › 2-Layer Sandwich › ERH-like fold › Enhancer of rudimentary 0.50 41.0 3.54e-01 100.0% 67.0%
ECOD (24)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3587703 101.1.14.0 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases 0.85 68.0 7.07e-01 94.5% 94.0%
2876 101.1.14.2 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › I-HmuI_NUMOD-like 0.81 69.0 6.37e-01 100.0% 73.9%
5009313 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.66 47.0 4.12e-01 100.0% 51.2%
3249480 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.64 43.0 3.75e-01 100.0% 47.5%
3932124 5050.1.1.32 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Acatn 0.62 41.0 2.69e-01 100.0% 15.2%
5062832 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.62 45.0 3.62e-01 100.0% 41.0%
3180640 2492.1.1.1 ↗ a+b three layers › Cytidine deaminase-like › Cytidine deaminase-like › Cytidine deaminase-like › dCMP_cyt_deam_1 0.61 45.0 3.26e-01 80.0% 71.9%
5083184 284.1.1.1 ↗ a+b two layers › FKBP-like › FKBP-like › FKBP-like › FKBP_C 0.59 51.0 3.93e-01 100.0% 88.7%
4945987 284.1.1.32 ↗ a+b two layers › FKBP-like › FKBP-like › FKBP-like › FKBP26_IF 0.59 50.0 4.16e-01 100.0% 82.9%
3883656 108.1.1.147 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › EF-hand_1, EF-hand_10 0.56 41.0 3.86e-01 80.0% 100.0%
3891185 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.55 35.0 3.45e-01 98.2% 60.0%
3540823 2484.1.1.175 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FGGY_N+FGGY_C 0.54 48.0 2.76e-01 100.0% 19.0%
3485346 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.54 38.0 3.48e-01 76.4% 86.7%
3407008 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.53 41.0 3.64e-01 90.9% 56.5%
3278358 284.3.1.2 ↗ a+b two layers › FKBP-like › Colicin E3 immunity protein › Colicin E3 immunity protein › DUF7683 0.53 48.0 4.31e-01 100.0% 94.7%
4861390 2484.1.1.6 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FGGY_N 0.53 46.0 2.97e-01 100.0% 32.1%
3600334 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.53 43.0 3.68e-01 90.9% 73.3%
3789432 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.53 40.0 2.37e-01 83.6% 92.8%
3252383 12.3.1.46 ↗ beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › ComC_SSD 0.52 44.0 2.95e-01 100.0% 42.1%
3927859 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.51 42.0 3.41e-01 90.9% 58.1%
3815248 376.1.2.2 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › Cysteine-rich domain › C1_2 0.50 41.0 2.87e-01 100.0% 35.3%
3533739 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.50 44.0 3.53e-01 98.2% 99.1%
185144 11.1.1.146 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF3244 0.50 40.0 3.44e-01 90.9% 61.7%
4382604 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.50 36.0 3.16e-01 87.3% 71.4%
D4 medium residues 106-178
PDB
Domain cluster: rep: IMGVR_UViG_3300045988_039364-3300045988-Ga0495776_000344_76889_77461__D110-188
CATH (30)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1u3eM02 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 0.77 57.0 5.95e-01 80.8% 83.8%
2x5pA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.63 36.0 3.19e-01 79.5% 39.4%
1cidA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 37.0 3.74e-01 82.2% 60.6%
6fwvA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.61 36.0 3.39e-01 80.8% 47.8%
3irzA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 37.0 3.40e-01 86.3% 47.5%
1t0yA00 3.10.20.90 Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1 0.58 38.0 3.60e-01 86.3% 54.4%
2mf9A00 3.10.50.40 Alpha Beta › Roll › Chitinase A; domain 3 › 0.58 41.0 3.18e-01 72.6% 48.4%
3jxvA02 3.10.50.40 Alpha Beta › Roll › Chitinase A; domain 3 › 0.58 41.0 3.52e-01 75.3% 68.6%
4dt4A01 3.10.50.40 Alpha Beta › Roll › Chitinase A; domain 3 › 0.58 41.0 4.06e-01 75.3% 89.9%
4mn5A00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.58 40.0 3.66e-01 74.0% 80.6%
2l6oA01 2.40.10.320 Mainly Beta › Beta Barrel › Thrombin, subunit H › Uncharacterised protein PF13642 yp_926445, N-terminal domain 0.57 36.0 3.62e-01 78.1% 62.5%
4p0dA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 37.0 3.17e-01 80.8% 42.6%
8bk6A01 3.10.50.40 Alpha Beta › Roll › Chitinase A; domain 3 › 0.56 40.0 3.51e-01 75.3% 70.9%
1ix5A00 3.10.50.40 Alpha Beta › Roll › Chitinase A; domain 3 › 0.55 40.0 3.23e-01 78.1% 92.1%
3gzkA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 35.0 3.48e-01 80.8% 60.8%
3jqwC00 2.60.120.380 Mainly Beta › Sandwich › Jelly Rolls › 0.55 33.0 2.78e-01 78.1% 36.4%
3p42A03 3.10.560.10 Alpha Beta › Roll › Outer membrane lipoprotein wza fold like › Outer membrane lipoprotein wza domain like 0.55 29.0 2.98e-01 74.0% 50.0%
4jgpA01 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.54 33.0 3.09e-01 79.5% 48.9%
2mm0A00 2.10.70.110 Mainly Beta › Ribbon › Complement Module; domain 1 › 0.54 39.0 4.15e-01 76.7% 98.4%
3f1sB02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.54 37.0 3.41e-01 86.3% 54.8%
3fedA02 3.50.30.30 Alpha Beta › 3-Layer(bba) Sandwich › Glucose Oxidase; domain 1 › 0.54 39.0 2.81e-01 78.1% 99.5%
3luqB00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.54 36.0 3.24e-01 71.2% 81.6%
4tweA02 3.50.30.30 Alpha Beta › 3-Layer(bba) Sandwich › Glucose Oxidase; domain 1 › 0.54 39.0 2.79e-01 78.1% 99.6%
2kfwA01 3.10.50.40 Alpha Beta › Roll › Chitinase A; domain 3 › 0.54 38.0 3.35e-01 75.3% 66.4%
4g5aA00 2.60.40.3080 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 34.0 3.11e-01 80.8% 48.5%
1ywlA00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.51 41.0 3.81e-01 90.4% 88.5%
2xqyA03 2.60.40.3190 Mainly Beta › Sandwich › Immunoglobulin-like › Herpesvirus glycoprotein H, C-terminal domain 0.51 37.0 3.06e-01 83.6% 42.1%
1ut9A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 37.0 3.36e-01 82.2% 57.1%
4kqdB00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.51 34.0 3.04e-01 71.2% 75.9%
3afgA03 2.60.120.380 Mainly Beta › Sandwich › Jelly Rolls › 0.51 32.0 2.90e-01 80.8% 46.1%
ECOD (26)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4414927 101.1.14.3 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › NUMOD1 0.78 60.0 6.14e-01 80.8% 88.4%
2876 101.1.14.2 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › I-HmuI_NUMOD-like 0.77 57.0 5.92e-01 80.8% 82.6%
4384880 101.1.14.3 ↗ alpha arrays › HTH › HTH › DNA-binding domain of intron-encoded endonucleases › NUMOD1 0.75 55.0 5.27e-01 78.1% 67.1%
4946799 101.1.11.0 ↗ alpha arrays › HTH › HTH › Ribbon-helix-helix 0.73 41.0 3.50e-01 76.7% 36.4%
3839138 2004.1.1.36 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Dynamin_N 0.63 37.0 2.56e-01 78.1% 16.5%
3998387 221.1.1.52 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › Ubiquitin_2 0.62 36.0 3.50e-01 78.1% 51.2%
3927867 11.1.4.70 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › NOMO1-like_1st 0.61 39.0 3.65e-01 83.6% 53.3%
4319035 11.1.1.608 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Por_Secre_tail 0.61 36.0 3.78e-01 79.5% 63.8%
5081326 11.1.1.608 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Por_Secre_tail 0.60 39.0 4.11e-01 83.6% 73.8%
5063052 11.1.1.1410 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › CarboxypepD_reg 0.59 36.0 3.39e-01 82.2% 50.0%
4942476 11.1.4.23 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › CarboxypepD_reg 0.58 36.0 3.53e-01 84.9% 57.5%
3933682 822.1.1.0 ↗ a+b two layers › GYF/BRK domain-like › GYF domain › GYF domain 0.58 35.0 3.07e-01 79.5% 38.3%
3695427 822.1.1.1 ↗ a+b two layers › GYF/BRK domain-like › GYF domain › GYF domain › GYF 0.58 37.0 3.68e-01 82.2% 62.7%
4956412 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 34.0 3.38e-01 82.2% 57.3%
3805835 4121.1.1.2 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › MRS2-like 0.56 43.0 3.00e-01 84.9% 29.8%
3881492 109.4.1.411 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TTC3_DZIP3_dom 0.55 41.0 2.78e-01 83.6% 21.0%
5032460 10.1.2.180 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › GOLD domain-like (DEPRECATED) › EMP24_GP25L 0.54 34.0 3.33e-01 83.6% 57.5%
3925735 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.54 37.0 3.29e-01 84.9% 50.5%
3798089 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.53 36.0 3.19e-01 83.6% 48.6%
3783891 10.32.1.4 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › EMP24_GP25L 0.52 32.0 2.82e-01 82.2% 39.1%
5080022 223.1.1.14 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_4 0.52 36.0 2.96e-01 72.6% 64.8%
5053089 223.1.1.14 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_4 0.51 35.0 3.13e-01 74.0% 75.7%
3435437 304.9.1.0 ↗ a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.51 41.0 3.82e-01 89.0% 94.7%
1310612 223.1.1.91 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › TraJ 0.51 34.0 3.04e-01 71.2% 75.9%
4557440 10.32.1.4 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like › EMP24_GP25L 0.50 32.0 2.85e-01 83.6% 43.8%
3992801 11.1.1.532 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › C6 0.50 33.0 3.11e-01 76.7% 55.6%