Back to structures

PHAGE-A6--js4906-27-3_S30_scaffold_5_curated_closed_complete_prodigal-single.1__X__X__00090

Bact-Vir

PHAGE-A6--js4906-27-3_S30_scaffold_5_curated_closed_complete_prodigal-single.1__X__X__00090

Identity

Kingdom:
phage

Quality

85.2 mean pLDDT

3D Structure

Domains

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

D1 high residues 45-107
PDB
Domain cluster: representative
CATH (52)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5b1aC01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.86 65.0 6.36e-01 93.7% 73.5%
2e5yA02 1.20.5.440 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › ATP synthase delta/epsilon subunit, C-terminal domain 0.82 56.0 6.58e-01 71.4% 100.0%
2lw1A00 1.10.287.380 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Valyl-tRNA synthetase, C-terminal domain 0.82 67.0 6.02e-01 88.9% 85.9%
3tu3B03 1.20.1050.100 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.80 55.0 3.91e-01 71.4% 33.5%
1zpyA00 6.10.140.1960 Special › Helix non-globular › Helix Hairpins › 0.79 70.0 6.19e-01 98.4% 76.9%
3r84B00 6.10.280.160 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Mediator of RNA polymerase II transcription subunit 22 0.78 64.0 5.93e-01 88.9% 91.3%
4e6nA02 6.10.140.1010 Special › Helix non-globular › Helix Hairpins › 0.78 64.0 6.30e-01 93.7% 84.8%
3sjqC00 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.78 58.0 5.39e-01 81.0% 80.0%
1un8A02 1.25.40.340 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › DhaL domain 0.77 62.0 4.29e-01 85.7% 28.1%
1lrzA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.76 62.0 6.31e-01 92.1% 90.3%
4h63K00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.76 64.0 5.51e-01 93.7% 63.3%
1ydxA02 1.10.287.1120 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Bipartite methylase S protein 0.74 63.0 5.65e-01 96.8% 92.2%
3k29A00 1.10.287.1700 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.74 62.0 4.56e-01 92.1% 74.5%
2dnxA00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.73 61.0 4.83e-01 93.7% 50.0%
4y9jA01 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.73 64.0 4.86e-01 100.0% 55.0%
3fxdB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.72 61.0 6.32e-01 93.7% 100.0%
4dwlA00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.72 59.0 4.94e-01 100.0% 52.8%
4gltA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.72 61.0 5.07e-01 96.8% 57.9%
7zxkC01 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.72 59.0 4.46e-01 90.5% 99.3%
1wa8A00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.72 59.0 5.13e-01 92.1% 72.7%
2qywA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.71 60.0 5.24e-01 93.7% 63.2%
2r9iA00 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.71 57.0 5.56e-01 88.9% 78.9%
4mk3A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.71 62.0 5.15e-01 100.0% 61.7%
1o5hA00 1.20.120.680 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Formiminotetrahydrofolate cyclodeaminase monomer, up-and-down helical bundle 0.70 59.0 4.13e-01 95.2% 29.5%
1b04A03 1.10.287.610 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.70 53.0 5.35e-01 85.7% 82.3%
2cazC00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.70 56.0 5.65e-01 87.3% 95.3%
4aflA00 6.10.140.1740 Special › Helix non-globular › Helix Hairpins › 0.70 59.0 5.01e-01 93.7% 59.8%
4id0A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.69 60.0 5.01e-01 100.0% 59.8%
3r2qA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.69 59.0 4.95e-01 100.0% 58.4%
6g94A00 1.20.950.20 Mainly Alpha › Up-down Bundle › Fumarate Reductase Cytochrome B subunit › Transmembrane di-heme cytochromes, Chain C 0.68 56.0 4.11e-01 92.1% 47.1%
1r2jA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.68 60.0 4.62e-01 100.0% 50.0%
1ni3A03 1.10.150.300 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Obg-related GTPase Ych/YyaF, coiled-coil domain 0.67 54.0 4.82e-01 88.9% 63.7%
4h63H01 1.20.58.1710 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 59.0 5.65e-01 96.8% 94.4%
4ikhA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.67 55.0 4.51e-01 96.8% 52.8%
3okqA00 1.20.58.1540 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Actin interacting protein 3, C-terminal domain 0.66 53.0 4.40e-01 93.7% 60.0%
2hh7A00 1.20.58.1000 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Metal-sensitive repressor, helix protomer 0.66 52.0 4.79e-01 96.8% 65.9%
5fhiA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.66 56.0 4.40e-01 96.8% 47.5%
4iggA01 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.66 52.0 5.20e-01 92.1% 97.0%
3qavA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.64 53.0 4.22e-01 96.8% 51.4%
4w4kA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.64 51.0 4.76e-01 92.1% 85.4%
1exzB00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.63 53.0 4.18e-01 100.0% 43.6%
8b6jF01 1.10.287.20 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Ubiquinol-cytochrome C reductase hinge domain 0.62 44.0 4.33e-01 76.2% 74.6%
2kg7B00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.62 44.0 3.86e-01 76.2% 54.6%
2pvqA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.61 51.0 4.46e-01 100.0% 62.3%
2mpkA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.61 46.0 4.38e-01 93.7% 70.3%
3e22A03 1.10.287.600 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.59 45.0 4.70e-01 84.1% 98.1%
2yksA02 1.20.58.390 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Neurotransmitter-gated ion-channel transmembrane domain 0.59 47.0 3.94e-01 92.1% 51.3%
3lphC00 6.10.140.630 Special › Helix non-globular › Helix Hairpins › 0.58 46.0 4.78e-01 90.5% 98.3%
4ri6A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.58 48.0 4.00e-01 96.8% 52.1%
3r0qA02 2.70.160.11 Mainly Beta › Distorted Sandwich › Hnrnp arginine n-methyltransferase1 › Hnrnp arginine n-methyltransferase1 0.57 49.0 3.35e-01 92.1% 93.3%
2ykgA03 1.20.1320.30 Mainly Alpha › Up-down Bundle › phosphoenolpyruvate carboxylase, domain 3 › 0.57 47.0 3.74e-01 93.7% 63.9%
3qowA01 1.10.260.60 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › 0.50 43.0 3.55e-01 100.0% 93.4%
ECOD (48)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
2141223 5055.1.1.1 extended segments › Small-conductance potassium channel › Small-conductance potassium channel › Small-conductance potassium channel › CaMBD 0.86 72.0 6.17e-01 88.9% 65.3%
4025148 4163.1.1.0 alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF1 N-terminal domain-like 0.83 70.0 5.37e-01 92.1% 53.3%
4959509 192.8.1.0 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.83 67.0 6.89e-01 87.3% 90.0%
3609435 3922.1.1.0 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 0.82 70.0 6.17e-01 93.7% 80.0%
None 0.81 68.0 4.61e-01 92.1% 28.2%
3702706 192.15.1.0 alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.81 68.0 6.25e-01 92.1% 86.3%
3471396 604.6.1.0 alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.78 63.0 5.44e-01 87.3% 61.1%
4949876 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 0.78 65.0 6.49e-01 92.1% 89.2%
4979114 150.1.1.0 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.77 65.0 5.17e-01 93.7% 67.2%
3387089 1075.4.1.1 alpha bundles › Type II ABC exporter transmembrane domain fold › Type I ABC exporter transmembrane domain fold › Type I ABC exporter transmembrane domain fold › ABC_membrane 0.76 65.0 4.13e-01 95.2% 21.6%
3611163 2004.1.1.480 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N, AAA_21, AAA_29 0.76 65.0 3.88e-01 93.7% 13.9%
4192664 622.4.1.0 alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related 0.76 64.0 4.06e-01 93.7% 21.0%
3370743 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 0.76 64.0 5.90e-01 92.1% 72.5%
3805996 192.10.1.7 alpha bundles › Long alpha-hairpin › DnaK suppressor protein DksA, alpha-hairpin domain › DnaK suppressor protein DksA, alpha-hairpin domain › HisKA 0.75 64.0 6.03e-01 92.1% 77.3%
4463756 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 0.75 64.0 6.16e-01 92.1% 82.9%
4968655 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.75 56.0 4.19e-01 81.0% 100.0%
4311175 304.48.1.0 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.75 46.0 2.95e-01 79.4% 14.4%
3755252 604.6.1.1 alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain › GAT 0.74 61.0 5.20e-01 92.1% 56.2%
3963355 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 0.74 61.0 5.80e-01 92.1% 86.7%
5006655 5069.1.1.2 alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › Ni_hydr_CYTB 0.73 63.0 4.34e-01 96.8% 31.2%
3514777 174.1.1.0 few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.73 63.0 4.91e-01 100.0% 44.3%
3883768 5086.1.1.101 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › SH3BP5 0.72 61.0 4.88e-01 93.7% 72.8%
4387171 603.5.1.18 alpha bundles › STAT-like › FlgN-like › FlgN-like › Med30 0.72 59.0 4.46e-01 92.1% 40.0%
4111212 622.4.1.30 alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related › ETR1_N 0.72 63.0 5.42e-01 100.0% 67.0%
3238851 3812.1.1.0 alpha bundles › Type III secretion protein YscE › Type III secretion protein YscE › Type III secretion protein YscE 0.72 59.0 5.00e-01 92.1% 59.0%
3947593 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 60.0 5.63e-01 95.2% 77.5%
4030407 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.71 61.0 5.81e-01 95.2% 81.3%
3990854 192.7.1.0 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.71 59.0 5.28e-01 92.1% 78.9%
4890998 148.1.3.28 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_lid_11 0.71 57.0 3.64e-01 92.1% 18.5%
3195005 604.1.1.0 alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.71 57.0 5.10e-01 88.9% 73.3%
4492444 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.71 55.0 5.32e-01 85.7% 75.7%
3621307 601.54.1.0 alpha bundles › Four-helical up-and-down bundle › low CO2-inducible protein LCI1 › low CO2-inducible protein LCI1 0.70 62.0 4.58e-01 100.0% 42.4%
3911171 192.7.1.44 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › SHCBP_N 0.70 58.0 5.24e-01 93.7% 67.8%
3709926 601.1.1.0 alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.69 56.0 4.79e-01 90.5% 59.0%
3952753 150.7.1.1 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › PE › PE › PE 0.69 53.0 5.02e-01 82.5% 92.0%
1197353 109.1.1.6 alpha superhelices › Repetitive alpha hairpins › Glutathione S-transferase (GST)-C › Glutathione S-transferase (GST)-C › GST_C_2 0.69 60.0 4.87e-01 100.0% 54.8%
3734442 192.8.1.35 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › DUF6594 0.69 56.0 4.52e-01 93.7% 47.7%
3598120 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 57.0 4.63e-01 93.7% 50.0%
4002563 192.8.1.303 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › Tmemb_cc2 0.67 56.0 4.08e-01 93.7% 35.0%
3612403 7015.1.1.0 alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain 0.67 60.0 4.57e-01 100.0% 45.5%
5069235 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.67 54.0 3.99e-01 93.7% 81.1%
4432932 3615.1.1.10 alpha bundles › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain › TMEM125 0.66 54.0 4.39e-01 96.8% 48.1%
1293726 150.7.1.1 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › PE › PE › PE 0.66 53.0 4.91e-01 92.1% 88.2%
4001550 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.65 52.0 4.99e-01 100.0% 76.0%
3506243 3602.1.1.3 alpha bundles › Kinase suppressor of Ras 1 helical hairpin domain › Kinase suppressor of Ras 1 helical hairpin domain › Kinase suppressor of Ras 1 helical hairpin domain › Enkurin 0.65 52.0 5.00e-01 92.1% 77.3%
4371144 3560.1.1.1 a+b complex topology › Mediator of RNA polymerase II transcription subunit 8 › Mediator of RNA polymerase II transcription subunit 8 › Mediator of RNA polymerase II transcription subunit 8 › Med8 0.65 53.0 3.95e-01 93.7% 34.7%
56798 150.7.1.0 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › PE › PE 0.63 50.0 4.82e-01 92.1% 89.5%
2574361 150.7.1.1 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › PE › PE › PE 0.60 49.0 4.71e-01 93.7% 91.9%