Back to structures

NC_052654.1__YP_009985052.1__JR319_gp130__00215

Bact-Vir

NC_052654.1__YP_009985052.1__JR319_gp130__00215

Identity

Accession:
NC_052654 ↗
Kingdom:
phage

Quality

68.4 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 high residues 9-67
PDB
Domain cluster: representative
CATH (59)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2lmgA00 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.85 64.0 5.88e-01 79.7% 67.6%
5b1oA00 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.85 64.0 6.26e-01 81.4% 73.8%
1x0tA01 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 0.83 59.0 5.93e-01 81.4% 73.8%
4nb5B02 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.82 64.0 6.28e-01 84.7% 98.4%
4iggA01 1.10.287.160 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HR1 repeat 0.81 68.0 6.56e-01 100.0% 82.1%
1x04A00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.79 68.0 4.64e-01 94.9% 28.0%
2psmA00 1.20.1250.70 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › Interleukin-15/Interleukin-21 0.78 58.0 4.62e-01 86.4% 40.2%
6r1nA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.78 66.0 5.52e-01 96.6% 65.0%
6zhiB02 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.77 56.0 5.04e-01 91.5% 55.4%
2cazD00 6.10.140.820 Special › Helix non-globular › Helix Hairpins › 0.77 61.0 6.14e-01 88.1% 100.0%
6xj1A01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.77 65.0 4.31e-01 96.6% 44.9%
2wmmA01 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 0.77 57.0 6.09e-01 79.7% 100.0%
2ic6A00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.77 66.0 6.20e-01 98.3% 78.9%
3lssA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.76 65.0 5.29e-01 96.6% 62.5%
3qo8A01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.76 63.0 5.23e-01 96.6% 51.9%
2lf0A01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.76 63.0 6.28e-01 93.2% 91.7%
1skvA00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.75 61.0 6.04e-01 96.6% 85.9%
5jrcA00 1.20.58.2140 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.75 59.0 4.17e-01 88.1% 28.0%
2cmrA00 1.20.58.1860 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.75 63.0 4.45e-01 96.6% 34.9%
2kw6A00 6.10.140.1300 Special › Helix non-globular › Helix Hairpins › 0.75 61.0 6.00e-01 96.6% 86.2%
6t0bc01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.75 61.0 5.63e-01 93.2% 76.9%
2gsqA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.74 62.0 5.13e-01 94.9% 51.9%
3fd9A03 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.74 62.0 5.87e-01 96.6% 80.8%
5dkoA02 1.10.3900.10 Mainly Alpha › Orthogonal Bundle › YacF-like › YacF-like 0.74 55.0 4.01e-01 81.4% 30.5%
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 0.74 56.0 6.01e-01 88.1% 100.0%
1z0pA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.74 59.0 5.61e-01 91.5% 78.1%
1lvfB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.74 60.0 5.14e-01 96.6% 65.4%
1wleA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.73 60.0 4.95e-01 94.9% 67.5%
2aj4B03 1.20.1440.340 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.73 57.0 4.20e-01 88.1% 54.3%
3nymA00 6.10.290.10 Special › Helix non-globular › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.73 63.0 5.00e-01 100.0% 48.4%
3wd6A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.72 61.0 4.82e-01 93.2% 50.0%
1ykeD00 6.10.280.10 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Mediator complex, subunit Med21 0.72 61.0 5.04e-01 98.3% 58.4%
3r84B00 6.10.280.160 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Mediator of RNA polymerase II transcription subunit 22 0.72 61.0 5.58e-01 98.3% 83.7%
4errB00 1.20.58.1190 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.72 62.0 5.56e-01 96.6% 68.7%
3n5lA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.72 58.0 5.94e-01 96.6% 98.2%
2mpnA00 6.10.140.1340 Special › Helix non-globular › Helix Hairpins › 0.72 63.0 6.03e-01 100.0% 91.2%
3rq9A00 1.10.287.2500 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.72 56.0 5.23e-01 93.2% 67.9%
4u1cA01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.71 51.0 5.35e-01 81.4% 88.5%
1gaxA05 1.10.287.380 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Valyl-tRNA synthetase, C-terminal domain 0.71 58.0 5.46e-01 93.2% 78.1%
3r84A00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.71 59.0 5.40e-01 96.6% 76.5%
1b48A02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.71 58.0 4.83e-01 94.9% 50.5%
1m5iA00 1.10.287.450 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.70 59.0 4.96e-01 96.6% 57.1%
3fxdB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 55.0 5.60e-01 89.8% 89.7%
1s5jA04 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.70 55.0 5.52e-01 91.5% 86.9%
1tj7A01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.70 52.0 4.35e-01 81.4% 47.6%
6f1eA01 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.69 52.0 4.03e-01 88.1% 36.0%
3nrxA00 1.20.58.1520 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.68 58.0 4.60e-01 96.6% 48.0%
1wa8A00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.68 56.0 4.77e-01 93.2% 56.6%
2i7uA00 6.10.250.1010 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.67 54.0 5.36e-01 91.5% 93.5%
2m6bA00 1.20.58.390 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Neurotransmitter-gated ion-channel transmembrane domain 0.67 57.0 4.27e-01 96.6% 94.0%
2wzkA03 1.20.1310.10 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Cullin Repeats 0.65 53.0 4.35e-01 89.8% 75.5%
1vibA00 1.10.287.120 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Neurotoxin B-IV-like 0.65 47.0 4.83e-01 83.1% 83.6%
4i9oA00 1.10.246.20 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › Coactivator CBP, KIX domain 0.63 44.0 4.09e-01 76.3% 56.4%
4od8D00 6.10.140.1880 Special › Helix non-globular › Helix Hairpins › 0.63 44.0 4.73e-01 81.4% 86.3%
2lpeA01 6.10.140.1120 Special › Helix non-globular › Helix Hairpins › 0.62 50.0 4.66e-01 94.9% 76.9%
5svlA01 1.10.287.940 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › atp-gated p2x4 ion channel 0.62 51.0 4.87e-01 91.5% 80.9%
2wgmA01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.60 48.0 4.49e-01 100.0% 72.0%
2b3tB01 6.10.140.1980 Special › Helix non-globular › Helix Hairpins › 0.59 47.0 4.66e-01 91.5% 83.1%
2jx4A01 6.10.140.460 Special › Helix non-globular › Helix Hairpins › 0.58 42.0 4.48e-01 81.4% 100.0%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3210948 192.6.1.0 alpha bundles › Long alpha-hairpin › Epsilon subunit of F1F0-ATP synthase C-terminal domain › Epsilon subunit of F1F0-ATP synthase C-terminal domain 0.84 66.0 5.93e-01 84.7% 73.8%
3912433 603.1.1.5 alpha bundles › STAT-like › t-snare proteins › t-snare proteins › Syntaxin-6_N 0.80 69.0 5.25e-01 96.6% 46.7%
5045370 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 0.80 66.0 6.60e-01 100.0% 91.7%
3754907 192.29.1.1 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB_dom 0.80 66.0 5.76e-01 96.6% 61.1%
3473420 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 0.80 68.0 4.62e-01 96.6% 90.2%
4652719 3291.1.1.0 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.79 67.0 5.78e-01 96.6% 77.9%
3725377 192.15.1.44 alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › DUF6604 0.79 67.0 5.86e-01 94.9% 65.6%
3535346 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 0.78 65.0 3.85e-01 96.6% 12.6%
3947717 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.78 67.0 4.90e-01 96.6% 38.1%
4982959 3922.1.1.357 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 › Auto_anti-p27 0.77 62.0 5.30e-01 93.2% 54.0%
3242106 3291.1.1.0 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.77 63.0 5.00e-01 93.2% 77.6%
3942444 5058.1.1.4 alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › COX4_pro 0.77 60.0 5.24e-01 86.4% 56.7%
3889547 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.76 64.0 4.51e-01 96.6% 53.7%
4005270 3718.1.1.15 alpha bundles › Flagellar protein fliT › Flagellar protein fliT › Flagellar protein fliT › COX4_pro 0.76 59.0 5.10e-01 86.4% 53.7%
149872 3291.1.1.1 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Snf7 0.76 64.0 5.86e-01 96.6% 73.4%
3967901 192.15.1.91 alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains › COX4_pro 0.76 59.0 5.17e-01 86.4% 56.7%
4522608 3812.1.1.15 alpha bundles › Type III secretion protein YscE › Type III secretion protein YscE › Type III secretion protein YscE › COX4_pro 0.76 59.0 5.16e-01 86.4% 56.7%
3477418 4992.1.1.12 extended segments › RelB-like › RelB-like › RelB-like › LIN9_C 0.75 64.0 5.55e-01 98.3% 77.9%
3618651 3291.1.1.0 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.75 64.0 5.73e-01 98.3% 68.2%
4025638 1189.1.1.0 alpha bundles › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor 0.74 61.0 4.23e-01 91.5% 29.7%
3355246 192.1.1.0 alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain 0.74 61.0 5.63e-01 96.6% 77.5%
3944950 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 0.74 59.0 5.74e-01 93.2% 81.5%
3460130 603.1.1.0 alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.74 61.0 5.60e-01 94.9% 73.8%
3541678 101.1.1.117 alpha arrays › HTH › HTH › Three-helical HTH › CHDCT2 0.73 60.0 5.21e-01 93.2% 58.9%
4051951 605.2.1.0 alpha duplicates or obligate multimers › ROP-like › Hypothetical protein D-63 › Hypothetical protein D-63 0.73 61.0 5.40e-01 96.6% 82.2%
5083098 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.73 63.0 5.35e-01 98.3% 62.0%
3840952 601.19.1.39 alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein › LIN9_C 0.73 60.0 5.63e-01 94.9% 78.7%
4129922 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.73 61.0 5.20e-01 96.6% 57.0%
3180119 604.5.1.0 alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) 0.72 59.0 5.31e-01 93.2% 64.7%
3446461 109.4.1.541 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › DUF4220 0.72 62.0 4.04e-01 100.0% 43.7%
3585354 192.29.1.0 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.72 59.0 5.26e-01 96.6% 65.6%
3298167 5086.1.1.62 alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › XH 0.71 58.0 4.57e-01 98.3% 42.9%
3929573 192.8.1.395 alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › CHDCT2 0.70 56.0 5.07e-01 96.6% 64.7%
3928221 4.1.1.310 beta barrels › SH3 › SH3 › SH3 › PF26050 0.69 56.0 4.36e-01 98.3% 39.3%
3592972 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.68 58.0 4.05e-01 96.6% 29.7%
4459223 605.1.1.162 alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › COX4_pro 0.68 58.0 5.07e-01 100.0% 63.4%
3326073 3291.1.1.0 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.67 55.0 4.63e-01 96.6% 53.6%
3570117 375.6.1.2 few secondary structure elements › Rubredoxin-like › FlhC-like › FlhC-like › PF31275 0.66 52.0 5.20e-01 86.4% 86.7%
3691750 376.1.1.8 few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › U-box 0.64 54.0 4.01e-01 93.2% 37.6%