Back to structures

NC_005284.1__NP_945088.1__phi1026bp58__00058

Bact-Vir

NC_005284.1__NP_945088.1__phi1026bp58__00058

Identity

Accession:
NC_005284 ↗
Kingdom:
phage

Quality

82.2 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 28-87
PDB
Domain cluster: representative
CATH (56)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2rklF00 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 0.90 59.0 6.34e-01 75.0% 78.8%
3zc0D00 1.20.58.2140 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.85 60.0 4.10e-01 80.0% 23.5%
5tqbB01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.85 65.0 3.98e-01 81.7% 15.7%
1j5wA02 1.20.58.180 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Class II aaRS and biotin synthetases; domain 2 0.84 60.0 5.52e-01 81.7% 58.4%
2fbaA00 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.84 61.0 3.50e-01 88.3% 9.3%
1yxrA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.83 61.0 5.62e-01 83.3% 62.2%
1j30A00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.82 62.0 4.67e-01 81.7% 42.6%
2e9xA01 1.20.58.1030 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.81 61.0 4.74e-01 81.7% 42.2%
2oo2A00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.80 59.0 5.47e-01 81.7% 61.8%
4akgA04 1.20.58.1120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Dynein motor heavy chain, linker domain, subdomain 4 0.79 69.0 5.11e-01 100.0% 43.6%
4q4hA01 1.20.1560.10 Mainly Alpha › Up-down Bundle › ABC transporter transmembrane region fold › ABC transporter type 1, transmembrane domain 0.78 58.0 3.66e-01 81.7% 17.6%
4m70I00 1.20.5.4130 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.78 58.0 4.82e-01 81.7% 59.3%
3pwfA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.78 58.0 4.53e-01 81.7% 42.7%
2jdiG01 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.77 58.0 5.86e-01 81.7% 80.3%
1yuzB01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.77 68.0 5.19e-01 100.0% 84.1%
1e52A00 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.76 54.0 5.61e-01 81.7% 80.4%
1gqeA01 1.20.58.410 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Release factor 0.76 66.0 5.37e-01 98.3% 87.6%
1tqgA00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.76 62.0 5.14e-01 100.0% 51.4%
1kfdA02 1.20.1060.10 Mainly Alpha › Up-down Bundle › Taq DNA Polymerase; Chain T, domain 4 › Taq DNA Polymerase; Chain T, domain 4 0.76 63.0 5.97e-01 91.7% 90.1%
1d9cA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.76 50.0 3.96e-01 71.7% 33.9%
2yb5F01 1.20.1280.250 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.75 54.0 4.82e-01 78.3% 53.5%
1wkbA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.74 55.0 4.40e-01 80.0% 43.0%
1yvwA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.74 54.0 4.70e-01 78.3% 54.3%
1jgcA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.73 63.0 4.68e-01 100.0% 72.5%
2gs4A00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.73 62.0 4.67e-01 100.0% 81.6%
5jajA03 1.20.1320.30 Mainly Alpha › Up-down Bundle › phosphoenolpyruvate carboxylase, domain 3 › 0.73 66.0 5.26e-01 100.0% 69.0%
1rv2D04 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.73 54.0 5.21e-01 81.7% 78.6%
3nymA00 6.10.290.10 Special › Helix non-globular › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.72 54.0 4.31e-01 81.7% 44.4%
6umqA01 1.20.930.60 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › 0.72 62.0 5.02e-01 100.0% 50.4%
2yxhA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.72 53.0 4.35e-01 81.7% 42.5%
3a98A02 1.20.1270.350 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Dedicator of cytokinesis N-terminal subdomain 0.72 61.0 5.52e-01 100.0% 74.7%
1luwA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.72 51.0 5.07e-01 76.7% 81.2%
1d2mA03 6.10.140.240 Special › Helix non-globular › Helix Hairpins › 0.71 53.0 5.17e-01 96.7% 72.7%
1vmgA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.71 51.0 4.63e-01 78.3% 56.1%
6h5hA00 1.10.150.110 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › DNA polymerase beta, N-terminal domain-like 0.71 57.0 5.44e-01 100.0% 74.6%
4hb1A00 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 48.0 5.30e-01 73.3% 100.0%
3k59A06 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.70 51.0 5.57e-01 85.0% 100.0%
1vh6A01 6.10.140.1940 Special › Helix non-globular › Helix Hairpins › 0.69 54.0 4.72e-01 90.0% 100.0%
2qtfA02 6.10.250.2860 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.69 49.0 5.25e-01 76.7% 97.9%
5b1aC01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.68 50.0 4.91e-01 81.7% 76.5%
3rlfF01 1.20.58.370 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › MalF N-terminal region-like 0.68 57.0 5.17e-01 100.0% 67.4%
2pmrA00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.68 58.0 5.42e-01 100.0% 77.6%
1iq0A03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.68 51.0 4.18e-01 81.7% 42.2%
3q15B00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.68 53.0 3.32e-01 86.7% 78.3%
2gscC00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.66 55.0 4.67e-01 100.0% 59.1%
2x1lA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.66 58.0 4.19e-01 100.0% 46.5%
1f6fA00 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.66 54.0 3.93e-01 95.0% 56.8%
4m0mA03 1.20.1270.430 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.65 55.0 5.04e-01 98.3% 72.2%
1rqgA04 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.64 56.0 4.22e-01 100.0% 48.3%
4aezI01 1.25.40.430 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.63 43.0 3.13e-01 73.3% 25.5%
5jc3A02 1.20.1320.30 Mainly Alpha › Up-down Bundle › phosphoenolpyruvate carboxylase, domain 3 › 0.61 54.0 4.25e-01 98.3% 71.4%
1oq4A00 1.10.620.20 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase, subunit A › Ribonucleotide Reductase, subunit A 0.61 46.0 2.92e-01 85.0% 14.7%
1gs0A01 1.20.142.10 Mainly Alpha › Up-down Bundle › Poly(ADP-ribose) Polymerase; domain 1 › Poly(ADP-ribose) polymerase, regulatory domain 0.61 51.0 4.10e-01 98.3% 90.7%
2uyyA02 1.10.1040.10 Mainly Alpha › Orthogonal Bundle › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 › N-(1-d-carboxylethyl)-l-norvaline Dehydrogenase; domain 2 0.58 45.0 3.70e-01 98.3% 43.1%
4ipeB02 3.30.230.80 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.54 41.0 3.08e-01 83.3% 59.4%
3a06B03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.54 40.0 3.57e-01 80.0% 56.8%
ECOD (42)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4993041 150.1.1.3 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Rubrerythrin 0.87 65.0 5.78e-01 81.7% 58.7%
1830108 2484.8.1.1 mixed a+b and a/b › Ribonuclease H-like › Separase pseudo-protease domain (PPD) › Separase pseudo-protease domain (PPD) › Peptidase_C50 0.85 65.0 4.08e-01 81.7% 18.1%
5030918 632.11.1.1 alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like › DUF357 0.84 61.0 5.53e-01 81.7% 57.5%
3703438 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 0.83 63.0 4.58e-01 81.7% 32.0%
3940514 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 0.83 65.0 4.77e-01 83.3% 41.3%
3286104 632.22.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.83 62.0 5.10e-01 81.7% 47.0%
3504805 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 0.82 72.0 5.50e-01 100.0% 65.7%
4219218 192.7.1.2 alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.80 60.0 4.91e-01 81.7% 47.3%
3409452 632.22.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.79 66.0 5.84e-01 90.0% 74.1%
3691023 109.4.1.353 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › MOR2-PAG1_N 0.79 53.0 3.57e-01 81.7% 19.5%
55685 150.1.1.0 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.78 72.0 5.30e-01 100.0% 78.1%
3611216 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.77 57.0 4.43e-01 83.3% 36.9%
4987985 3684.1.1.0 alpha complex topology › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like 0.77 57.0 4.78e-01 81.7% 52.4%
3451533 192.29.1.237 alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › DUF3755 0.76 57.0 5.22e-01 81.7% 66.3%
4970979 633.21.1.0 alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 0.76 66.0 5.51e-01 100.0% 59.0%
4962838 225.1.1.3 a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.74 62.0 4.19e-01 91.7% 78.6%
5014075 632.11.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.74 63.0 5.64e-01 100.0% 71.1%
4947161 150.1.1.3 alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Rubrerythrin 0.74 63.0 4.84e-01 100.0% 83.4%
5075122 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 0.72 53.0 4.22e-01 81.7% 42.3%
3985675 3579.1.1.30 extended segments › NADH-quinone oxidoreductase subunit J › NADH-quinone oxidoreductase subunit J › NADH-quinone oxidoreductase subunit J › Imp-YgjV 0.72 51.0 3.94e-01 78.3% 32.9%
5056430 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.72 50.0 4.83e-01 75.0% 67.1%
4941476 632.11.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.72 61.0 5.61e-01 100.0% 81.2%
3987421 3843.1.1.0 alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K 0.71 59.0 5.74e-01 100.0% 81.5%
4601603 632.15.1.4 alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) › HSP70 0.71 51.0 4.73e-01 80.0% 58.7%
3312887 4025.1.1.1 alpha complex topology › alpha-helical domain in nickel-iron hydrogenase, large subunit › alpha-helical domain in nickel-iron hydrogenase, large subunit › alpha-helical domain in nickel-iron hydrogenase, large subunit › Complex1_49kDa 0.71 58.0 4.43e-01 96.7% 40.6%
3944935 6155.2.1.3 alpha duplicates or obligate multimers › TOG superfamily › PnuC › PnuC › Imp-YgjV 0.71 50.0 3.73e-01 78.3% 28.7%
4946271 601.7.1.0 alpha bundles › Four-helical up-and-down bundle › HEPN › Nucleotidyltransferase substrate binding subunit/domain 0.70 51.0 4.15e-01 80.0% 40.9%
4085606 632.22.1.1 alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats › EzrA 0.70 61.0 5.07e-01 100.0% 75.5%
4029448 3755.3.1.0 alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.70 51.0 4.01e-01 78.3% 76.8%
3956423 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 0.68 49.0 4.06e-01 80.0% 47.8%
3286721 2003.1.5.66 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_11 0.67 56.0 3.83e-01 100.0% 91.0%
3292425 3291.1.1.4 alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › PspA_IM30 0.67 50.0 3.45e-01 81.7% 65.9%
3875941 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 0.67 56.0 4.20e-01 98.3% 55.2%
5056592 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.66 54.0 3.36e-01 93.3% 21.1%
5054157 632.11.1.1 alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like › DUF357 0.66 54.0 5.08e-01 100.0% 74.7%
3462665 604.12.1.0 alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.65 43.0 4.59e-01 70.0% 88.0%
3330281 4992.1.1.0 extended segments › RelB-like › RelB-like › RelB-like 0.64 54.0 4.55e-01 100.0% 67.3%
3999857 632.6.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Plasmid maintenance system epsilon/zeta, antidote epsilon subunit › Plasmid maintenance system epsilon/zeta, antidote epsilon subunit 0.61 46.0 4.36e-01 96.7% 68.0%
3927235 632.7.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain 0.61 43.0 4.20e-01 96.7% 67.1%
5038830 375.1.1.26 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › Rpr2 0.60 42.0 3.67e-01 76.7% 46.0%
4618805 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 0.58 42.0 4.36e-01 81.7% 94.5%
4152566 4274.1.1.1 extended segments › Transmembrane helices in MalF N-terminal region › Transmembrane helices in MalF N-terminal region › Transmembrane helices in MalF N-terminal region › MalF_N_TM 0.58 45.0 4.63e-01 93.3% 96.4%