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MK533143.1__QBX06395.1__API480_32__00032

Bact-Vir

MK533143.1__QBX06395.1__API480_32__00032

Identity

Accession:
MK533143 ↗
Kingdom:
phage

Quality

75.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Paenibacillus_phage_vB_PlaP_API480

TaxID: 2530020

Cluster

Singleton — not in a non-trivial cluster

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 1-65
PDB
Domain cluster: representative
CATH (27)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2l1lB00 1.20.1440.250 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.85 58.0 4.55e-01 78.5% 36.2%
6tkvA01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.82 64.0 6.37e-01 100.0% 80.9%
4q20A01 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.79 67.0 6.23e-01 98.5% 74.4%
1z0jB00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.79 55.0 6.10e-01 75.4% 94.1%
3h6pC00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.77 61.0 6.47e-01 84.6% 100.0%
4gczA03 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.77 66.0 6.60e-01 93.8% 95.4%
4m0mA03 1.20.1270.430 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.76 53.0 4.95e-01 76.9% 59.5%
3b2eF00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.76 64.0 6.56e-01 92.3% 98.4%
2r9iA00 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.76 66.0 6.42e-01 98.5% 95.8%
3lphC00 6.10.140.630 Special › Helix non-globular › Helix Hairpins › 0.76 60.0 6.25e-01 86.2% 96.6%
2gv9A05 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.76 57.0 5.94e-01 96.9% 91.5%
1sg2A00 3.30.910.20 Alpha Beta › 2-Layer Sandwich › Protein Binding, DinI Protein; Chain A › Skp domain 0.75 66.0 5.16e-01 100.0% 49.6%
1m5iA00 1.10.287.450 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.74 67.0 5.68e-01 100.0% 100.0%
2gsqA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.73 57.0 4.84e-01 86.2% 56.5%
3ctwB00 1.10.8.930 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Protein of unknown function DUF1465 0.72 63.0 5.11e-01 95.4% 56.7%
2c41C01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.72 59.0 4.54e-01 90.8% 40.3%
4dlqA02 1.25.40.610 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.72 59.0 5.27e-01 93.8% 63.2%
4fxdA04 3.90.1600.10 Alpha Beta › Alpha-Beta Complex › Palm domain of DNA polymerase › B family DNA polymerase, palm domain 0.71 57.0 4.40e-01 90.8% 56.9%
8jx6A02 2.30.30.780 Mainly Beta › Roll › SH3 type barrels. › 0.69 45.0 3.89e-01 90.8% 41.7%
4l0rB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.69 59.0 5.69e-01 93.8% 91.8%
2lf0A01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.69 55.0 5.75e-01 90.8% 96.7%
3hinA02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.69 46.0 4.89e-01 87.7% 81.8%
4b6xA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.68 57.0 5.64e-01 95.4% 100.0%
2vx2G02 1.10.12.10 Mainly Alpha › Orthogonal Bundle › Lyase 2-enoyl-coa Hydratase; Chain A, domain 2 › Lyase 2-enoyl-coa Hydratase, Chain A, domain 2 0.67 46.0 4.89e-01 75.4% 83.6%
2y1vA04 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.67 50.0 3.65e-01 84.6% 28.6%
3bhnA00 3.40.50.880 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Class I glutamine amidotransferase (GATase) domain 0.66 58.0 4.03e-01 96.9% 47.4%
4errB00 1.20.58.1190 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.64 53.0 5.03e-01 100.0% 83.1%
ECOD (40)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3700672 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.90 84.0 6.79e-01 100.0% 60.0%
3864552 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.88 81.0 6.85e-01 98.5% 71.0%
4650373 604.1.1.169 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Med14 0.85 69.0 5.87e-01 100.0% 55.2%
4978586 604.9.1.0 ↗ alpha bundles › Spectrin repeat-like › Ribosomal protein S20 › Ribosomal protein S20 0.84 73.0 6.02e-01 93.8% 59.1%
3180974 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.83 62.0 6.70e-01 84.6% 94.5%
3474600 4207.1.2.48 ↗ alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › MED7 hinge region › Med14 0.82 68.0 5.83e-01 100.0% 59.0%
3915818 4207.1.1.35 ↗ alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › RNA polymerase II holoenzyme component SRB7 (MED21) › Med14 0.81 67.0 5.80e-01 100.0% 59.0%
5064072 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 0.81 66.0 5.86e-01 87.7% 71.1%
3962893 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.80 71.0 6.30e-01 100.0% 69.5%
3336158 70.3.1.0 ↗ beta barrels › beta-clip › SET domain-like › SET domain-like 0.80 59.0 4.46e-01 89.2% 34.5%
4969335 3352.1.1.0 ↗ alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain 0.79 62.0 3.86e-01 100.0% 15.9%
3917938 4177.1.1.5 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › Vps5 0.78 70.0 4.83e-01 100.0% 73.5%
3393794 3922.1.1.211 ↗ 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 › DRC7_C 0.78 68.0 5.43e-01 100.0% 54.1%
4405928 5086.1.1.196 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › HH_YknX 0.78 67.0 6.57e-01 100.0% 88.6%
3204772 192.1.1.31 ↗ alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain › Cep57_MT_bd 0.78 70.0 6.05e-01 100.0% 66.0%
3917917 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.78 68.0 5.74e-01 100.0% 61.8%
3497911 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.77 66.0 5.22e-01 98.5% 45.9%
3448294 3826.1.1.33 ↗ alpha bundles › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › Copper-sensitive operon repressor (CsoR) › eIF-4B 0.77 65.0 5.94e-01 92.3% 70.6%
3614068 5055.1.1.0 ↗ extended segments › Small-conductance potassium channel › Small-conductance potassium channel › Small-conductance potassium channel 0.77 67.0 6.27e-01 96.9% 81.2%
4992337 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.76 67.0 5.31e-01 100.0% 61.5%
3927560 192.8.1.0 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain 0.76 61.0 6.25e-01 89.2% 100.0%
3433708 192.29.1.217 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › MCAfunc 0.76 66.0 5.78e-01 100.0% 73.0%
3298709 605.1.1.141 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › Rx_N 0.75 66.0 5.34e-01 98.5% 53.6%
4026159 4970.1.1.0 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.75 53.0 5.84e-01 75.4% 100.0%
3286299 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.74 65.0 5.48e-01 98.5% 60.0%
4780326 601.19.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein 0.74 66.0 4.72e-01 100.0% 33.9%
4220356 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 0.74 66.0 4.15e-01 100.0% 64.2%
4943086 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.73 52.0 5.09e-01 75.4% 72.9%
4039014 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.73 64.0 5.37e-01 98.5% 60.0%
3850093 4099.1.1.11 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › Med14 0.72 61.0 5.41e-01 98.5% 66.0%
3927285 1008.1.1.51 ↗ alpha bundles › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain › BRCC36 C-terminal helical domain › Med14 0.72 62.0 5.25e-01 100.0% 57.4%
4336724 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.72 63.0 5.32e-01 100.0% 95.5%
5047074 2004.1.1.87 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › SMC_N 0.71 63.0 3.90e-01 98.5% 17.8%
4984327 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.70 61.0 5.23e-01 100.0% 94.3%
5012794 4333.1.1.0 ↗ a+b complex topology › DNA methylase specificity domain › DNA methylase specificity domain › DNA methylase specificity domain 0.69 61.0 3.80e-01 100.0% 70.7%
3183519 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.68 51.0 5.37e-01 86.2% 100.0%
3848250 605.1.1.325 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › CCDC28 0.68 56.0 5.35e-01 98.5% 78.8%
1821875 4970.1.1.1 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_B 0.65 50.0 5.17e-01 92.3% 94.9%
3731974 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.63 55.0 4.68e-01 100.0% 90.9%
4671 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.63 52.0 4.53e-01 98.5% 59.1%