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OK562670.1__UFJ83601.1__ply2008005c_43__00043

Bact-Vir

OK562670.1__UFJ83601.1__ply2008005c_43__00043

Identity

Accession:
OK562670 ↗
Kingdom:
phage

Quality

90.1 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Shangdongvirus› Stenotrophomonas_phage_vB_SM_ytsc_ply2008005c

TaxID: 2894587

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 3-39
PDB
Domain cluster: representative
CATH (48)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2a26B01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.95 81.0 7.59e-01 100.0% 77.3%
4fvmA06 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.93 78.0 7.13e-01 100.0% 70.8%
4l0rB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.93 78.0 6.08e-01 100.0% 46.6%
1rq0A01 6.10.140.160 Special › Helix non-globular › Helix Hairpins › 0.90 82.0 6.17e-01 100.0% 62.7%
1yzmA00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.90 81.0 7.50e-01 100.0% 80.4%
2qqyA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.90 81.0 5.30e-01 100.0% 26.8%
2cazC00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.89 80.0 6.58e-01 100.0% 75.0%
1z0jB00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.89 80.0 7.13e-01 100.0% 72.5%
3sjqC00 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.89 78.0 6.00e-01 100.0% 50.0%
2yxyA01 1.10.287.880 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Hypothetical protein YfhH domain 0.88 79.0 7.11e-01 100.0% 74.0%
3b2eF00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.88 78.0 6.52e-01 100.0% 59.7%
3kyiA00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.87 78.0 5.23e-01 100.0% 28.9%
2r9iA00 1.10.287.80 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ATP synthase, gamma subunit, helix hairpin domain 0.87 71.0 5.73e-01 100.0% 47.9%
2cwoA01 1.20.58.1200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › RNA silencing suppressor P21, N-terminal domain 0.87 73.0 5.91e-01 100.0% 50.0%
7nc3F01 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.86 76.0 5.28e-01 100.0% 36.0%
3kwoA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.86 76.0 4.95e-01 100.0% 24.8%
1m5iA00 1.10.287.450 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.86 74.0 5.30e-01 97.3% 94.3%
4djgB00 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 0.85 69.0 6.35e-01 100.0% 70.2%
2lf0A01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.85 74.0 6.34e-01 100.0% 61.7%
4gltA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.85 72.0 5.11e-01 100.0% 36.0%
1hqoA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.85 74.0 5.00e-01 100.0% 31.3%
4nswB01 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.81 65.0 3.92e-01 100.0% 14.1%
3k59A06 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.79 66.0 6.22e-01 100.0% 80.9%
4h63H01 1.20.58.1710 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.78 64.0 5.33e-01 100.0% 56.9%
3lphC00 6.10.140.630 Special › Helix non-globular › Helix Hairpins › 0.76 58.0 5.15e-01 89.2% 100.0%
3l09A01 1.20.58.1460 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.74 58.0 4.49e-01 100.0% 44.9%
3r84B00 6.10.280.160 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Mediator of RNA polymerase II transcription subunit 22 0.72 55.0 4.62e-01 100.0% 91.3%
1z5zA02 1.20.120.850 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SWI2/SNF2 ATPases, N-terminal domain 0.71 58.0 4.78e-01 100.0% 52.6%
2vyrA00 1.10.245.10 Mainly Alpha › Orthogonal Bundle › MDM2 › SWIB/MDM2 domain 0.70 49.0 3.80e-01 89.2% 32.9%
2f93B00 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.69 59.0 5.36e-01 100.0% 74.5%
3l1nA01 6.10.140.790 Special › Helix non-globular › Helix Hairpins › 0.69 55.0 5.13e-01 100.0% 72.5%
3fxdB00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.68 52.0 4.79e-01 100.0% 93.1%
3txsC01 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.68 52.0 4.46e-01 100.0% 50.7%
2elcA01 1.20.970.10 Mainly Alpha › Up-down Bundle › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain A, domain 3 › Transferase, Pyrimidine Nucleoside Phosphorylase; Chain C 0.68 53.0 4.43e-01 89.2% 53.7%
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 0.68 51.0 5.00e-01 100.0% 79.2%
4jfcA02 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 53.0 4.73e-01 97.3% 60.7%
3m1cB01 3.30.390.170 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › 0.66 50.0 3.85e-01 97.3% 33.9%
4akrA01 3.30.1140.60 Alpha Beta › 2-Layer Sandwich › Ribosomal protein S3 C-terminal domain › F-actin capping protein, alpha subunit 0.65 52.0 3.92e-01 97.3% 35.8%
2d5wA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.63 51.0 3.24e-01 100.0% 19.0%
4i1eA03 1.25.10.30 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › IP3 receptor type 1 binding core, RIH domain 0.63 54.0 3.65e-01 100.0% 54.7%
2j5iA02 6.10.250.2850 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.63 50.0 4.99e-01 97.3% 100.0%
2ckoA02 3.90.1200.10 Alpha Beta › Alpha-Beta Complex › Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 › Aminoglycoside phosphotransferase (APH), C-terminal lobe 0.62 52.0 3.15e-01 100.0% 44.4%
1jeiA00 1.10.720.40 Mainly Alpha › Orthogonal Bundle › Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 › 0.62 42.0 3.86e-01 89.2% 50.9%
2ic6A00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.62 45.0 4.01e-01 100.0% 59.2%
1t16A00 2.40.160.60 Mainly Beta › Beta Barrel › Porin › Outer membrane protein transport protein (OMPP1/FadL/TodX) 0.60 46.0 2.71e-01 100.0% 8.7%
3qkaE02 1.10.287.2460 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.59 47.0 4.59e-01 97.3% 90.7%
7ce1A01 1.10.260.40 Mainly Alpha › Orthogonal Bundle › 434 Repressor (Amino-terminal Domain) › lambda repressor-like DNA-binding domains 0.58 48.0 4.35e-01 94.6% 80.8%
3keyA01 1.10.10.1080 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Stn1, N-terminal wHTH domain 0.56 46.0 3.56e-01 94.6% 80.5%
ECOD (50)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3904130 1203.1.2.1 ↗ alpha bundles › Shroom domain 2 › Shroom domain 2 › Human SD2 › ASD2 0.99 93.0 6.17e-01 100.0% 30.8%
3703494 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.99 92.0 6.25e-01 100.0% 33.6%
3910027 614.1.1.3 ↗ alpha duplicates or obligate multimers › L27 domain › L27 domain › L27 domain › L27_1 0.98 90.0 7.26e-01 100.0% 60.0%
3989824 192.1.1.0 ↗ alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain 0.97 89.0 7.90e-01 100.0% 74.0%
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 0.96 89.0 6.25e-01 100.0% 37.0%
3710592 604.6.1.0 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.94 86.0 6.18e-01 100.0% 38.9%
3662390 632.15.1.3 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) › GAUT_1 0.94 85.0 6.11e-01 100.0% 38.9%
3595108 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 0.94 84.0 6.19e-01 100.0% 41.1%
4445940 192.4.1.1 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) › Ribosomal_L29 0.93 85.0 6.64e-01 100.0% 60.3%
3280086 101.1.2.48 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR 0.93 84.0 5.22e-01 100.0% 20.6%
4507133 3710.1.1.1 ↗ alpha bundles › Golgi to ER traffic protein 1 cytosolic domain › Golgi to ER traffic protein 1 cytosolic domain › Golgi to ER traffic protein 1 cytosolic domain › CHD5 0.92 84.0 6.05e-01 100.0% 53.7%
4438372 2004.1.1.5 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.92 84.0 4.79e-01 100.0% 12.1%
4300890 3710.1.1.1 ↗ alpha bundles › Golgi to ER traffic protein 1 cytosolic domain › Golgi to ER traffic protein 1 cytosolic domain › Golgi to ER traffic protein 1 cytosolic domain › CHD5 0.92 84.0 6.82e-01 100.0% 56.9%
4381724 3710.1.1.1 ↗ alpha bundles › Golgi to ER traffic protein 1 cytosolic domain › Golgi to ER traffic protein 1 cytosolic domain › Golgi to ER traffic protein 1 cytosolic domain › CHD5 0.92 84.0 6.02e-01 100.0% 38.9%
4884100 5001.1.1.9 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › TAS2R 0.91 82.0 4.79e-01 100.0% 13.8%
3964450 607.1.1.1 ↗ alpha arrays › Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain › Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain › Enzyme I of the PEP:sugar phosphotransferase system HPr-binding (sub)domain › PEP-utilisers_N 0.91 82.0 5.57e-01 100.0% 33.3%
3237324 3710.1.1.1 ↗ alpha bundles › Golgi to ER traffic protein 1 cytosolic domain › Golgi to ER traffic protein 1 cytosolic domain › Golgi to ER traffic protein 1 cytosolic domain › CHD5 0.91 84.0 6.96e-01 100.0% 61.7%
3377582 632.21.1.4 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Helical bundle domain in endo-beta-N-acetylglucosaminidase F2 › Helical bundle domain in endo-beta-N-acetylglucosaminidase F2 › GAUT_1 0.91 79.0 5.80e-01 100.0% 38.9%
3926919 3710.1.1.0 ↗ alpha bundles › Golgi to ER traffic protein 1 cytosolic domain › Golgi to ER traffic protein 1 cytosolic domain › Golgi to ER traffic protein 1 cytosolic domain 0.91 82.0 6.89e-01 100.0% 61.7%
4838801 3710.1.1.1 ↗ alpha bundles › Golgi to ER traffic protein 1 cytosolic domain › Golgi to ER traffic protein 1 cytosolic domain › Golgi to ER traffic protein 1 cytosolic domain › CHD5 0.90 83.0 6.69e-01 100.0% 56.9%
165192 150.1.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin › Ferritin 0.90 81.0 5.29e-01 100.0% 26.6%
3998044 4177.1.1.8 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR_3 0.89 76.0 4.53e-01 100.0% 14.2%
4670545 3711.1.1.61 ↗ alpha bundles › LTXXQ motif family protein › LTXXQ motif family protein › LTXXQ motif family protein › CHD5 0.89 80.0 5.91e-01 100.0% 41.1%
3776620 3710.1.1.1 ↗ alpha bundles › Golgi to ER traffic protein 1 cytosolic domain › Golgi to ER traffic protein 1 cytosolic domain › Golgi to ER traffic protein 1 cytosolic domain › CHD5 0.89 80.0 5.07e-01 100.0% 21.9%
3744786 3710.1.1.1 ↗ alpha bundles › Golgi to ER traffic protein 1 cytosolic domain › Golgi to ER traffic protein 1 cytosolic domain › Golgi to ER traffic protein 1 cytosolic domain › CHD5 0.89 81.0 5.84e-01 100.0% 38.9%
3693025 3710.1.1.1 ↗ alpha bundles › Golgi to ER traffic protein 1 cytosolic domain › Golgi to ER traffic protein 1 cytosolic domain › Golgi to ER traffic protein 1 cytosolic domain › CHD5 0.89 79.0 6.68e-01 100.0% 61.7%
3507551 192.5.1.0 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat 0.89 78.0 5.72e-01 100.0% 38.9%
4128596 3710.1.1.1 ↗ alpha bundles › Golgi to ER traffic protein 1 cytosolic domain › Golgi to ER traffic protein 1 cytosolic domain › Golgi to ER traffic protein 1 cytosolic domain › CHD5 0.89 80.0 6.53e-01 100.0% 56.9%
3638319 192.7.1.56 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › CHD5 0.88 77.0 5.57e-01 100.0% 37.0%
3600712 192.5.1.0 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat 0.87 76.0 5.79e-01 100.0% 43.5%
3536875 4177.1.1.1 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › FCH 0.87 74.0 4.37e-01 100.0% 13.0%
3646439 192.8.1.263 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › DUF7615 0.87 76.0 5.79e-01 100.0% 43.5%
3884763 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.87 77.0 5.05e-01 100.0% 26.2%
3934925 604.3.1.0 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.86 68.0 5.28e-01 100.0% 41.2%
3175356 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.85 73.0 4.67e-01 100.0% 32.0%
3363809 4177.1.1.8 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR_3 0.85 71.0 4.27e-01 100.0% 14.5%
3782240 4177.1.1.8 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR_3 0.84 70.0 4.21e-01 100.0% 14.5%
3867484 4177.1.1.8 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR_3 0.83 69.0 4.13e-01 100.0% 23.4%
3495807 4177.1.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.83 67.0 4.06e-01 100.0% 14.5%
4218502 605.1.1.279 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › Spo7 0.82 71.0 5.13e-01 100.0% 35.2%
3178943 4177.1.1.8 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR_3 0.81 66.0 4.11e-01 100.0% 16.8%
3635651 109.4.1.907 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › M-HEAT_ATR 0.81 69.0 4.77e-01 100.0% 29.6%
4402331 3236.1.1.5 ↗ alpha complex topology › Cation-proton antiporter › Cation-proton antiporter (CPA) › Cation-proton antiporter (CPA) › Na_H_antiport_1 0.80 67.0 3.80e-01 100.0% 8.8%
3261777 4177.1.1.8 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › BAR_3 0.78 62.0 3.90e-01 100.0% 16.4%
4984419 2498.1.1.10 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M48 0.76 60.0 3.74e-01 100.0% 14.9%
4413603 218.1.1.8 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › HrcA 0.75 63.0 4.73e-01 100.0% 37.0%
3754265 603.1.1.187 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › DNA_repr_REX1B 0.75 59.0 4.53e-01 100.0% 37.8%
3516452 378.1.1.0 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases 0.68 56.0 3.52e-01 100.0% 19.1%
4201482 605.1.1.331 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › DUF3654 0.65 51.0 4.06e-01 100.0% 40.0%
3389798 2006.1.4.0 ↗ a/b three-layered sandwiches › HAD domain-like › HAD domain-related › PIN domain-like 0.63 46.0 3.87e-01 83.8% 45.7%