Back to structures

NC_070779.1__YP_010843924.1__PP427_gp068__00068

Bact-Vir

NC_070779.1__YP_010843924.1__PP427_gp068__00068

Identity

Accession:
NC_070779 ↗
Kingdom:
phage

Quality

80.8 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 medium residues 89-146
PDB
Domain cluster: representative
CATH (49)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1a36A04 1.10.132.10 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › 0.81 61.0 4.25e-01 84.5% 26.9%
4kjmA02 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.78 53.0 5.45e-01 82.8% 74.5%
1ij5A01 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.77 60.0 5.48e-01 84.5% 64.5%
4iloA00 1.10.287.1490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.76 61.0 3.97e-01 86.2% 21.6%
3qo8A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.75 59.0 4.78e-01 86.2% 46.2%
3txsC01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.75 59.0 5.46e-01 86.2% 66.7%
3lssA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.75 60.0 4.74e-01 86.2% 47.3%
3tklB01 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.75 58.0 5.75e-01 84.5% 82.3%
4ip8A00 1.10.132.110 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Serum amyloid A protein 0.74 60.0 4.94e-01 91.4% 49.5%
1t72A02 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.74 60.0 5.06e-01 93.1% 53.1%
2odmA00 1.10.287.750 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › SO2669-like 0.74 56.0 5.05e-01 89.7% 59.5%
6xxvC00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.74 61.0 4.91e-01 100.0% 47.7%
2lm9A00 1.20.58.970 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.74 58.0 4.90e-01 86.2% 60.4%
2m6uA00 1.20.81.20 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › 0.73 59.0 5.35e-01 93.1% 64.6%
1lrzA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 56.0 5.48e-01 84.5% 77.4%
1gaxA05 1.10.287.380 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Valyl-tRNA synthetase, C-terminal domain 0.72 57.0 5.27e-01 84.5% 75.3%
4e4eA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.72 54.0 5.12e-01 84.5% 67.6%
4q5qA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.71 57.0 4.64e-01 86.2% 49.5%
4l8iB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.71 62.0 5.04e-01 100.0% 52.7%
1t72A01 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.71 59.0 4.71e-01 93.1% 47.0%
1lvfB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.71 54.0 4.40e-01 86.2% 45.2%
7ymiZ01 1.10.287.740 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Photosystem II PsbZ, reaction centre 0.71 51.0 5.18e-01 79.3% 77.6%
1wp7A00 1.10.287.770 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YojJ-like 0.70 58.0 5.64e-01 91.4% 81.2%
2rp4A00 6.10.280.60 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Transcription factor p53, C-terminal domain 0.70 52.0 4.94e-01 84.5% 66.2%
1hr5A00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.70 49.0 5.24e-01 77.6% 89.6%
4hr1A00 1.20.1270.410 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.70 58.0 4.64e-01 93.1% 68.6%
2f93B00 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.70 54.0 5.74e-01 94.8% 96.1%
1cpyA02 1.10.287.410 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.70 51.0 4.74e-01 81.0% 62.5%
4abxA02 6.10.140.1090 Special › Helix non-globular › Helix Hairpins › 0.69 53.0 4.66e-01 84.5% 71.3%
3vm9A02 6.10.140.2110 Special › Helix non-globular › Helix Hairpins › 0.69 53.0 5.41e-01 91.4% 89.5%
3q5dA02 1.20.58.420 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › AHSP 0.69 60.0 5.07e-01 98.3% 60.8%
1kf6C00 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.69 53.0 4.10e-01 84.5% 38.5%
1bhaA00 1.10.287.170 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.68 53.0 5.06e-01 84.5% 71.6%
3eo8A00 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.68 54.0 3.71e-01 100.0% 24.2%
3a7mA01 1.20.58.380 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Flagellar protein flit. 0.67 50.0 4.15e-01 84.5% 43.6%
2xubA05 6.10.140.1450 Special › Helix non-globular › Helix Hairpins › 0.66 56.0 4.71e-01 93.1% 88.5%
1xfiA02 1.20.1700.10 Mainly Alpha › Up-down Bundle › AF1104-like › AF1104-like 0.66 55.0 4.88e-01 98.3% 80.0%
4dciA00 6.10.140.1110 Special › Helix non-globular › Helix Hairpins › 0.64 58.0 4.29e-01 100.0% 40.8%
4yvoA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.64 43.0 3.43e-01 79.3% 33.6%
1f7uA02 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.64 46.0 3.68e-01 82.8% 36.8%
4h63K00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.64 45.0 3.96e-01 79.3% 52.0%
2bkkC02 3.90.1200.10 Alpha Beta › Alpha-Beta Complex › Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 › Aminoglycoside phosphotransferase (APH), C-terminal lobe 0.62 50.0 3.62e-01 89.7% 74.6%
2e8gA01 1.20.1440.150 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.60 50.0 4.04e-01 100.0% 48.4%
1d2mA03 6.10.140.240 Special › Helix non-globular › Helix Hairpins › 0.60 46.0 4.48e-01 89.7% 92.4%
4oe8C00 1.10.8.1170 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.59 52.0 4.59e-01 100.0% 71.3%
2o5hA00 1.10.3510.10 Mainly Alpha › Orthogonal Bundle › NMB0513-like › NMB0513-like 0.59 49.0 3.79e-01 94.8% 41.4%
2oq1A02 1.10.930.10 Mainly Alpha › Orthogonal Bundle › Syk Kinase; Chain A, domain 2 › Syk Kinase; Chain A, domain 2 0.57 41.0 4.52e-01 94.8% 97.8%
5b1aC01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.55 44.0 4.23e-01 91.4% 91.2%
2fi1A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.54 38.0 3.71e-01 74.1% 100.0%
ECOD (42)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3602948 5058.1.1.16 alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › MS_channel_1st_1 0.86 75.0 6.83e-01 100.0% 73.3%
3395314 601.15.1.0 alpha bundles › Four-helical up-and-down bundle › Proteasome activator reg(alpha) › Proteasome activator reg(alpha) 0.85 69.0 4.88e-01 86.2% 32.3%
4948156 2004.5.1.0 a/b three-layered sandwiches › P-loop domains-like › Differentially expressed in normal cells and neoplasia (DENN) domain › Differentially expressed in normal cells and neoplasia (DENN) domain 0.85 73.0 4.67e-01 100.0% 22.0%
5077870 2498.1.1.10 mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M48 0.82 73.0 4.85e-01 100.0% 26.8%
5077354 2004.5.1.0 a/b three-layered sandwiches › P-loop domains-like › Differentially expressed in normal cells and neoplasia (DENN) domain › Differentially expressed in normal cells and neoplasia (DENN) domain 0.81 70.0 4.40e-01 100.0% 20.0%
5056476 5058.1.1.0 alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.79 71.0 6.49e-01 100.0% 90.7%
3961347 150.5.1.53 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › PPE 0.77 65.0 5.66e-01 91.4% 63.5%
3264784 2003.1.1.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.77 62.0 3.59e-01 86.2% 11.3%
3265477 5082.1.1.1 alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation_efflux 0.76 69.0 4.58e-01 100.0% 61.8%
4937584 5058.1.1.0 alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region 0.75 66.0 6.11e-01 100.0% 78.7%
4937313 5041.1.1.0 extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C 0.75 65.0 5.66e-01 100.0% 65.6%
3885007 3922.1.1.67 alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Val_tRNA-synt_C 0.75 60.0 5.63e-01 86.2% 80.0%
5031927 5057.1.1.0 alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore 0.74 65.0 5.71e-01 98.3% 72.9%
4299170 192.7.1.4 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Val_tRNA-synt_C 0.73 58.0 5.47e-01 86.2% 80.0%
3214887 605.1.1.0 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.73 63.0 6.46e-01 93.1% 100.0%
3785340 7581.1.1.3 a/b three-layered sandwiches › Thiolase-like › Thiolase-like › Thiolase-like › ketoacyl-synt,Ketoacyl-synt_C 0.72 59.0 3.30e-01 100.0% 7.2%
5045310 605.1.1.1 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.72 56.0 5.34e-01 86.2% 72.9%
3770340 5041.1.1.2 extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › TMEM169 0.72 61.0 5.11e-01 100.0% 56.2%
3953372 150.5.1.1 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like › WXG100 0.71 63.0 5.28e-01 98.3% 59.2%
5060491 5086.1.1.0 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.71 59.0 4.59e-01 93.1% 43.3%
3958129 150.5.1.0 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.71 63.0 5.52e-01 98.3% 68.2%
4960850 5041.1.1.0 extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C 0.71 58.0 5.78e-01 91.4% 91.7%
2075297 3559.1.1.0 a+b complex topology › Mediator of RNA polymerase II transcription subunit 22 › Mediator of RNA polymerase II transcription subunit 22 › Mediator of RNA polymerase II transcription subunit 22 0.71 56.0 4.41e-01 86.2% 64.7%
5009792 150.5.1.0 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.71 57.0 5.50e-01 91.4% 80.0%
4034278 5043.1.1.0 extended segments › Sensor proteins transmembrane domains › Htr2 transmembrane domain-like › Htr2 transmembrane domain-like 0.70 60.0 6.00e-01 100.0% 96.7%
4831662 5043.1.1.1 extended segments › Sensor proteins transmembrane domains › Htr2 transmembrane domain-like › Htr2 transmembrane domain-like › Htr2 0.69 58.0 5.66e-01 98.3% 89.4%
3256502 5086.1.1.0 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.68 56.0 3.68e-01 93.1% 22.2%
3991544 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.68 52.0 4.45e-01 86.2% 73.0%
3284949 150.1.1.0 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.68 57.0 5.47e-01 100.0% 85.7%
3896102 150.1.1.100 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › TMD0_ABC 0.68 60.0 4.16e-01 100.0% 63.1%
3906813 2004.1.1.26 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Kinesin 0.68 52.0 3.21e-01 86.2% 14.5%
4179286 547.1.1.1 alpha duplicates or obligate multimers › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › GlutR_dimer 0.68 58.0 5.21e-01 100.0% 84.7%
4029754 605.1.1.0 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.67 59.0 5.22e-01 100.0% 69.4%
5042923 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.67 60.0 4.81e-01 100.0% 88.7%
3215185 5057.1.1.1 alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neur_chan_memb 0.67 54.0 4.14e-01 93.1% 59.7%
3220993 5057.1.1.0 alpha bundles › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore › Neurotransmitter-gated ion-channel transmembrane pore 0.67 53.0 4.12e-01 93.1% 59.7%
3941043 605.1.1.211 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › ATG9 0.66 57.0 3.37e-01 100.0% 22.4%
4327215 547.1.1.1 alpha duplicates or obligate multimers › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › Glutamyl tRNA-reductase dimerization domain › GlutR_dimer 0.66 57.0 4.58e-01 100.0% 49.6%
144301 5041.1.1.1 extended segments › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › F1F0 ATP synthase subunit C › ATP-synt_C 0.64 52.0 4.89e-01 98.3% 72.6%
4013967 2004.1.1.184 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_11 0.64 52.0 3.12e-01 93.1% 11.7%
4660205 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.59 50.0 3.90e-01 98.3% 68.9%
3709217 574.1.1.1 alpha bundles › Surp module (SWAP domain) › Surp module (SWAP domain) › Surp module (SWAP domain) › Surp 0.54 39.0 3.75e-01 79.3% 67.1%