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NC_005856.1__YP_006580.1__P1_gp114__00110

Bact-Vir

NC_005856.1__YP_006580.1__P1_gp114__00110

Identity

Accession:
NC_005856 ↗
Kingdom:
phage

Quality

71.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Punavirus› Escherichia_phage_P1

TaxID: 2886926

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 1-36
PDB
Domain cluster: representative
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4dciA00 6.10.140.1110 Special › Helix non-globular › Helix Hairpins › 0.89 79.0 5.12e-01 100.0% 26.5%
3k2nA00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.88 75.0 4.73e-01 97.2% 20.3%
2nn4A00 1.10.287.760 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › YqgQ-like 0.86 75.0 6.27e-01 100.0% 66.1%
4hkaA02 1.10.287.3810 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.86 72.0 6.55e-01 100.0% 72.5%
4di1C02 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 0.86 73.0 7.05e-01 100.0% 87.8%
2j5iA02 6.10.250.2850 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.86 73.0 7.29e-01 100.0% 94.7%
1zoyD00 1.20.1300.10 Mainly Alpha › Up-down Bundle › 3 helical TM bundles of succinate and fumarate reductases › Fumarate reductase/succinate dehydrogenase, transmembrane subunit 0.84 70.0 5.13e-01 100.0% 36.3%
4adnA01 1.20.1280.250 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.84 70.0 5.42e-01 100.0% 44.7%
4hteA01 1.20.58.1730 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.84 72.0 4.80e-01 100.0% 25.9%
7vkcA01 1.10.1070.20 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 › 0.84 73.0 4.70e-01 100.0% 23.0%
1tmxB00 2.60.130.10 Mainly Beta › Sandwich › Protocatechuate 3,4-Dioxygenase, subunit A › Aromatic compound dioxygenase 0.83 69.0 4.06e-01 100.0% 12.5%
2l8kA00 3.30.1330.220 Alpha Beta › 2-Layer Sandwich › 60s Ribosomal Protein L30; Chain: A; › Arterivirus nonstructural protein 7 alpha 0.83 69.0 4.76e-01 100.0% 28.5%
2yqyA00 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.83 71.0 4.84e-01 100.0% 77.8%
4jylA02 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 0.83 69.0 6.36e-01 100.0% 73.5%
4kp3C00 1.20.58.1770 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.82 68.0 5.37e-01 100.0% 44.4%
3besR03 6.10.140.1480 Special › Helix non-globular › Helix Hairpins › 0.82 68.0 6.05e-01 100.0% 64.3%
2ig3A00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.80 65.0 4.58e-01 100.0% 28.3%
1dciA02 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 0.77 62.0 5.40e-01 100.0% 57.1%
1l8nA03 3.90.1330.10 Alpha Beta › Alpha-Beta Complex › Alpha-d-glucuronidase, C-terminal Domain › Alpha-glucuronidase, C-terminal domain 0.77 65.0 4.06e-01 100.0% 17.6%
7b9cA02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.77 57.0 3.31e-01 100.0% 8.5%
2m6uA00 1.20.81.20 Mainly Alpha › Up-down Bundle › Receptor-associated Protein › 0.76 58.0 4.78e-01 100.0% 45.1%
2f93B00 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.76 59.0 5.52e-01 100.0% 70.6%
2lm4A01 1.10.150.250 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Flavinator of succinate dehydrogenase 0.75 58.0 4.43e-01 91.7% 40.2%
1tjlA00 1.20.120.910 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › DksA, coiled-coil domain 0.72 63.0 4.22e-01 100.0% 27.6%
1lrzA03 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 60.0 5.09e-01 100.0% 66.1%
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 0.70 56.0 5.28e-01 100.0% 83.3%
3m1cB01 3.30.390.170 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › 0.68 56.0 4.09e-01 97.2% 34.9%
8igrI01 2.40.270.10 Mainly Beta › Beta Barrel › Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; Domain 6 › DNA-directed RNA polymerase, subunit 2, domain 6 0.66 55.0 3.60e-01 100.0% 22.2%
1nafA02 1.20.58.160 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.66 57.0 4.29e-01 97.2% 41.2%
2x1lB02 2.170.220.10 Mainly Beta › Beta Complex › Methionyl-trna Synthetase; domain 2 › 0.61 49.0 4.01e-01 97.2% 46.1%
1go3F02 6.10.140.10 Special › Helix non-globular › Helix Hairpins › 0.59 47.0 4.35e-01 97.2% 70.2%
1skvA00 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.58 42.0 3.87e-01 97.2% 100.0%
ECOD (17)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3244309 5054.1.1.0 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels 0.92 83.0 4.87e-01 100.0% 14.7%
3623989 323.1.1.6 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › Carn_acyltransf 0.91 82.0 5.22e-01 100.0% 24.0%
4666568 109.3.1.2 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › Ank,Ank_2 0.87 74.0 4.21e-01 100.0% 10.3%
3412881 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.86 76.0 5.80e-01 100.0% 72.5%
3263335 198.1.1.2 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_2,SapB_1 0.85 71.0 5.52e-01 100.0% 43.8%
3879791 378.1.1.0 ↗ few secondary structure elements › His-Me finger endonucleases › His-Me finger endonucleases › His-Me finger endonucleases 0.85 72.0 4.39e-01 100.0% 16.0%
197868 614.1.1.0 ↗ alpha duplicates or obligate multimers › L27 domain › L27 domain › L27 domain 0.82 68.0 6.24e-01 100.0% 70.6%
3261605 198.1.1.2 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like › SapB_2,SapB_1 0.81 65.0 5.11e-01 100.0% 42.5%
3583325 4082.1.1.0 ↗ alpha duplicates or obligate multimers › Hairy Orange domain › Hairy Orange domain › Hairy Orange domain 0.79 69.0 5.69e-01 100.0% 67.7%
3535165 7023.1.1.0 ↗ alpha bundles › helical ridge domain of D-alanyl transfer protein › helical ridge domain of D-alanyl transfer protein › helical ridge domain of D-alanyl transfer protein 0.77 61.0 4.39e-01 100.0% 30.0%
4323124 109.3.1.2 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › Ank,Ank_2 0.76 59.0 3.51e-01 100.0% 10.9%
4624218 301.6.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › Tubulin C-terminal domain-like › Tubulin C-terminal domain-like 0.73 59.0 3.87e-01 100.0% 20.6%
4002696 7023.1.1.0 ↗ alpha bundles › helical ridge domain of D-alanyl transfer protein › helical ridge domain of D-alanyl transfer protein › helical ridge domain of D-alanyl transfer protein 0.72 54.0 4.03e-01 100.0% 30.8%
1007238 3846.1.1.1 ↗ alpha bundles › IcmR › IcmR › IcmR › IcmR 0.71 60.0 5.22e-01 100.0% 71.2%
4171351 1.1.5.44 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › SecDF_P1_head 0.71 58.0 3.86e-01 100.0% 23.6%
4024235 2004.1.1.14 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › GTP_EFTU 0.70 55.0 3.36e-01 100.0% 12.5%
3503627 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.67 51.0 5.19e-01 100.0% 100.0%