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NC_009813.1__YP_001468764.1__LiPB054_gp60__00060

Bact-Vir

NC_009813.1__YP_001468764.1__LiPB054_gp60__00060

Identity

Accession:
NC_009813 ↗
Kingdom:
phage

Quality

93.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Listeria_phage_B054

TaxID: 330397

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 3-57
PDB
Domain cluster: representative
CATH (30)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2mh3A00 4.10.280.10 Few Secondary Structures › Irregular › MYOD Basic-Helix-Loop-Helix Domain, subunit B › Helix-loop-helix DNA-binding domain 0.80 57.0 5.29e-01 76.4% 60.0%
2jnsA01 1.20.1270.220 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.76 52.0 4.58e-01 72.7% 77.8%
2el7A02 1.10.240.10 Mainly Alpha › Orthogonal Bundle › Tyrosyl-Transfer RNA Synthetase › Tyrosyl-Transfer RNA Synthetase 0.71 48.0 4.04e-01 70.9% 78.7%
3nwoA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.70 48.0 2.99e-01 72.7% 14.0%
2pmrA00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.68 50.0 4.53e-01 80.0% 92.1%
4kxfB02 1.10.1900.50 Mainly Alpha › Orthogonal Bundle › c-terminal domain of poly(a) binding protein › 0.65 51.0 5.08e-01 89.1% 100.0%
2wl8C00 1.20.120.900 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Pex19, mPTS binding domain 0.63 45.0 3.54e-01 74.5% 78.0%
7ml0M01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.63 45.0 3.98e-01 76.4% 100.0%
2oo2A00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.62 44.0 4.07e-01 78.2% 78.9%
2dbgA00 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.62 45.0 3.74e-01 80.0% 41.7%
2l09A01 1.10.8.550 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Proto-chlorophyllide reductase 57 kD subunit B 0.62 45.0 4.58e-01 80.0% 96.2%
1rp3G02 1.20.140.160 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › PhyR, sigma-like (SL) domain 0.61 46.0 3.36e-01 80.0% 35.2%
2yn7A00 1.10.3160.10 Mainly Alpha › Orthogonal Bundle › Bbcrasp-1 › Bbcrasp-1 0.61 50.0 3.48e-01 98.2% 63.6%
2xkoA02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.60 41.0 3.45e-01 70.9% 100.0%
2ex3B02 1.20.1270.230 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › DNA terminal protein Gp3, priming domain 0.60 50.0 4.45e-01 94.5% 82.7%
2d1hB00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.60 40.0 3.46e-01 72.7% 92.9%
1wj7A01 1.10.8.10 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain 0.59 47.0 4.60e-01 89.1% 80.0%
4nqwA02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.59 45.0 4.32e-01 81.8% 79.7%
3rguB00 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 0.59 40.0 3.55e-01 72.7% 82.8%
5fgmA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.59 41.0 3.88e-01 72.7% 83.1%
1uxtA01 3.40.605.10 Alpha Beta › 3-Layer(aba) Sandwich › Aldehyde Dehydrogenase; Chain A, domain 1 › Aldehyde Dehydrogenase; Chain A, domain 1 0.58 42.0 2.68e-01 78.2% 48.0%
3vfzB00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.58 46.0 4.39e-01 85.5% 76.2%
1lp1A00 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 0.56 41.0 4.17e-01 85.5% 96.4%
6zhiB02 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.56 39.0 3.50e-01 76.4% 84.3%
3nuwA02 3.30.420.310 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 2-keto-3-deoxy-galactonokinase, C-terminal domain 0.55 43.0 3.02e-01 90.9% 39.0%
3l8rA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.53 39.0 3.25e-01 80.0% 85.3%
1rykA00 1.10.1470.10 Mainly Alpha › Orthogonal Bundle › Protein Yjbj; Chain: A; › YjbJ 0.53 36.0 3.50e-01 92.7% 60.9%
2j49A00 1.25.40.500 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › TFIID subunit TAF5, NTD2 domain 0.51 40.0 3.09e-01 89.1% 96.3%
4tq1A03 1.10.246.190 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › Autophagy protein Apg5, helix rich domain 0.51 38.0 3.78e-01 87.3% 100.0%
3rfwA02 6.10.140.970 Special › Helix non-globular › Helix Hairpins › 0.51 35.0 3.03e-01 78.2% 48.2%
ECOD (23)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3230329 105.1.1.0 ↗ alpha duplicates or obligate multimers › HLH-like › HLH, helix-loop-helix DNA-binding domain › HLH, helix-loop-helix DNA-binding domain 0.86 58.0 5.87e-01 70.9% 70.9%
3525386 197.1.1.8 ↗ alpha bundles › Acyl-CoA binding protein-like › Acyl-CoA binding protein-like › Acyl-CoA binding protein-like › PF26570 0.71 50.0 4.60e-01 76.4% 86.7%
4263879 632.7.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › HSP70 0.68 50.0 4.00e-01 80.0% 61.7%
3676971 143.1.1.3 ↗ alpha arrays › PABP domain-like › PABC(PABP) domain › PABC(PABP) domain › MLLE_2 0.65 54.0 5.25e-01 100.0% 100.0%
3929290 614.1.1.0 ↗ alpha duplicates or obligate multimers › L27 domain › L27 domain › L27 domain 0.65 47.0 4.40e-01 78.2% 88.6%
4962704 3317.1.1.8 ↗ alpha arrays › KorB C-terminal domain-like › KorB C-terminal domain › KorB C-terminal domain › DUF7119 0.64 53.0 5.05e-01 94.5% 84.6%
3661336 143.1.1.3 ↗ alpha arrays › PABP domain-like › PABC(PABP) domain › PABC(PABP) domain › MLLE_2 0.64 53.0 4.81e-01 98.2% 81.0%
3969413 101.1.4.0 ↗ alpha arrays › HTH › HTH › tetra-helical, lambda repressor-like 0.64 45.0 4.24e-01 76.4% 95.7%
4039740 3317.1.1.2 ↗ alpha arrays › KorB C-terminal domain-like › KorB C-terminal domain › KorB C-terminal domain › HTH_ParB 0.63 54.0 5.13e-01 96.4% 84.6%
3683174 143.1.1.0 ↗ alpha arrays › PABP domain-like › PABC(PABP) domain › PABC(PABP) domain 0.63 52.0 5.16e-01 96.4% 100.0%
5059799 3317.1.1.0 ↗ alpha arrays › KorB C-terminal domain-like › KorB C-terminal domain › KorB C-terminal domain 0.61 51.0 4.00e-01 96.4% 88.0%
3964247 5065.1.1.2 ↗ alpha bundles › Type II ABC importer transmembrane domain fold › Type II ABC importer transmembrane domain fold › Type II ABC importer transmembrane domain fold › FecCD 0.60 43.0 2.68e-01 76.4% 28.3%
3179896 143.1.1.0 ↗ alpha arrays › PABP domain-like › PABC(PABP) domain › PABC(PABP) domain 0.59 51.0 4.99e-01 96.4% 96.7%
3817587 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.59 46.0 4.69e-01 90.9% 100.0%
3643148 632.3.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Phosphoprotein XD domain › Phosphoprotein XD domain 0.59 43.0 4.38e-01 87.3% 100.0%
3655991 632.2.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Bacterial immunoglobulin/albumin-binding domains › Bacterial immunoglobulin/albumin-binding domains 0.58 48.0 4.85e-01 92.7% 100.0%
4240705 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 0.55 42.0 3.72e-01 87.3% 89.4%
3241303 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 0.55 37.0 3.44e-01 74.5% 87.5%
3569037 632.7.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › HSP70 0.54 38.0 3.35e-01 76.4% 77.8%
2085920 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.54 44.0 2.76e-01 96.4% 94.0%
5005181 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.54 39.0 2.81e-01 80.0% 92.0%
5009535 148.1.3.410 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › DUF6955 0.53 44.0 3.68e-01 96.4% 91.0%
4591513 130.1.1.0 ↗ alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › LEM/SAP HeH motif 0.53 36.0 3.38e-01 74.5% 90.7%