←Back to structures

NC_060137.1__YP_010246706.1__L3Y25_gp047__00047

Bact-Vir

NC_060137.1__YP_010246706.1__L3Y25_gp047__00047

Identity

Accession:
NC_060137 ↗
Kingdom:
phage

Quality

77.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Octobienvirus› Gordonia_phage_Syleon

TaxID: 2653718

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 131-191
PDB
Domain cluster: rep: MH316566.1__AWY03875.1__SEA_NEDARYA_58__00056__D165-231
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2zylA01 2.102.10.10 Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain 0.62 47.0 3.77e-01 86.9% 80.0%
4dxkA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.61 46.0 3.72e-01 83.6% 93.6%
2p84A02 2.30.30.290 Mainly Beta › Roll › SH3 type barrels. › YopX-like domains 0.58 44.0 4.23e-01 98.4% 74.0%
4z32C02 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.56 46.0 3.94e-01 91.8% 85.9%
4gi3C00 3.30.60.30 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.54 32.0 3.30e-01 83.6% 59.6%
3be3A00 2.30.30.320 Mainly Beta › Roll › SH3 type barrels. › DUF1653-like domain 0.54 42.0 3.97e-01 90.2% 92.1%
1wcdJ01 2.60.120.20 Mainly Beta › Sandwich › Jelly Rolls › 0.53 41.0 2.63e-01 83.6% 57.7%
1fguB02 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.53 41.0 3.37e-01 88.5% 78.2%
2gu1A02 3.10.450.350 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.52 40.0 3.37e-01 83.6% 80.8%
1okjA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.52 37.0 3.30e-01 78.7% 97.9%
1z1bA01 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.52 35.0 3.61e-01 82.0% 75.4%
4f3nA00 3.40.50.12710 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.51 39.0 2.45e-01 85.2% 71.9%
ECOD (10)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3214264 376.1.1.21 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_2 0.63 43.0 3.84e-01 70.5% 58.9%
3282690 219.1.1.8 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › NLPC_P60 0.61 45.0 3.76e-01 100.0% 42.5%
119219 3119.1.1.1 ↗ few secondary structure elements › CopK › CopK › CopK › CopK 0.59 39.0 3.71e-01 82.0% 56.8%
3593335 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.57 44.0 2.90e-01 86.9% 28.6%
5032759 9.23.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Hypothetical protein BT_0869 › Hypothetical protein BT_0869 0.56 45.0 4.09e-01 90.2% 95.2%
3799828 207.1.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats 0.54 38.0 2.55e-01 98.4% 16.3%
4420259 11.1.1.88 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › CBM9_1 0.54 45.0 3.29e-01 100.0% 75.4%
3649175 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.53 42.0 2.60e-01 96.7% 14.8%
3923157 376.1.1.27 ↗ few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box › zf-RING_5 0.51 32.0 3.53e-01 72.1% 78.0%
4880562 5.1.3.26 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › BNR_2 0.51 44.0 2.66e-01 100.0% 17.8%
D2 medium residues 5-54
PDB
D3 medium residues 57-120
PDB
Domain cluster: rep: JN698994.1__AER47606.1__DS6A_52__00052__D76-144
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3lphC00 6.10.140.630 Special › Helix non-globular › Helix Hairpins › 0.76 40.0 4.22e-01 79.7% 56.9%
1kblA05 1.20.80.30 Mainly Alpha › Up-down Bundle › Acyl-CoA Binding Protein › 0.68 52.0 4.65e-01 82.8% 66.3%
1irxA04 1.10.10.770 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.67 48.0 4.03e-01 89.1% 44.4%
2yevC00 6.10.280.110 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.60 42.0 4.25e-01 81.2% 73.0%
4arvA02 3.40.50.1240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphoglycerate mutase-like 0.59 48.0 4.00e-01 96.9% 62.7%
3k7dA03 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.57 46.0 3.55e-01 85.9% 52.2%
3whjA00 6.10.140.1710 Special › Helix non-globular › Helix Hairpins › 0.57 42.0 3.47e-01 78.1% 58.6%
2yqzA02 1.10.8.900 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.56 41.0 4.03e-01 78.1% 88.2%
1ulyA02 1.10.20.10 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A 0.53 45.0 3.96e-01 98.4% 68.3%
ECOD (5)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3270180 5063.1.1.0 ↗ alpha bundles › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK › Photosystem I reaction center subunit X, PsaK 0.63 45.0 3.99e-01 87.5% 53.3%
4014485 5044.1.1.0 ↗ extended segments › PsbZ-like › PsbZ-like › PsbZ-like 0.59 45.0 3.89e-01 84.4% 53.7%
3400028 3843.1.1.30 ↗ alpha complex topology › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › NADH-quinone oxidoreductase subunit K › DUF4781 0.58 40.0 3.64e-01 79.7% 54.1%
3754031 4120.1.1.36 ↗ few secondary structure elements › Tim10/DDP › Tim10/DDP › Tim10/DDP › cwf21 0.54 43.0 3.79e-01 85.9% 58.9%
3270265 223.2.1.20 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like › Fuz_longin_1 0.53 45.0 3.62e-01 100.0% 98.5%