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NC_029120.1__YP_009226852.1__AXI88_gp20__00020

Bact-Vir

NC_029120.1__YP_009226852.1__AXI88_gp20__00020

Identity

Accession:
NC_029120 ↗
Kingdom:
phage

Quality

79.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Diegovirus› Shigella_phage_75/02_Stx

TaxID: 1416032

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 (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2rdcA00 1.10.287.800 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › protein ne1242 0.85 60.0 4.41e-01 74.5% 31.6%
6nmnA02 1.20.120.330 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2 0.71 52.0 3.94e-01 87.3% 33.6%
3k2oB02 1.20.1280.270 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.70 52.0 5.60e-01 81.8% 100.0%
4w4kA00 1.10.287.850 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › HP0062-like domain 0.69 55.0 4.76e-01 85.5% 64.6%
6cgvM01 1.20.120.1500 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Pre-hexon-linking protein IIIa 0.65 50.0 3.82e-01 85.5% 40.3%
6r1nA01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.65 51.0 4.07e-01 94.5% 44.7%
4wzxA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.64 53.0 4.85e-01 92.7% 88.0%
2a2cA03 1.20.1440.340 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.64 55.0 4.20e-01 100.0% 78.3%
3hjlA03 1.20.5.2020 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.64 43.0 4.66e-01 78.2% 97.6%
5b1oA00 1.10.287.130 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Signal transduction histidine kinase, dimerisation/phosphotransfer (DHp) domain 0.64 46.0 4.38e-01 81.8% 64.6%
6ynwH01 1.20.20.10 Mainly Alpha › Up-down Bundle › F1FO ATP Synthase › F1F0 ATP synthase subunit C 0.63 49.0 4.44e-01 85.5% 74.3%
1vk0A00 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.62 55.0 3.73e-01 100.0% 96.0%
2wwwC01 1.20.5.170 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.61 47.0 4.77e-01 92.7% 100.0%
6gy8A01 1.20.1170.10 Mainly Alpha › Up-down Bundle › Hemolysin E; Chain: A; › 0.60 54.0 3.27e-01 98.2% 81.0%
5fhiA02 1.20.1050.10 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.60 47.0 3.49e-01 87.3% 33.8%
2p67A01 1.20.5.170 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.59 44.0 4.48e-01 89.1% 90.4%
2lpeA01 6.10.140.1120 Special › Helix non-globular › Helix Hairpins › 0.59 48.0 4.31e-01 98.2% 65.4%
1v4aA01 1.10.4050.10 Mainly Alpha › Orthogonal Bundle › Nucleotidyltransferase substrate binding subunit/domain fold › Glutamine synthase adenylyltransferase GlnE 0.58 52.0 4.11e-01 98.2% 57.8%
4x5mA00 1.20.1280.290 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.58 51.0 4.41e-01 100.0% 80.2%
2iexA02 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 0.54 37.0 3.80e-01 72.7% 90.2%
3dpuA03 1.10.10.2200 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.50 41.0 3.76e-01 94.5% 77.3%
ECOD (13)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3623190 174.1.1.31 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › DUF7027 0.74 56.0 3.97e-01 85.5% 28.1%
3825757 101.35.1.23 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX › Ovate 0.73 65.0 6.17e-01 100.0% 93.8%
4965021 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.71 52.0 5.21e-01 85.5% 76.4%
3350539 192.23.1.6 ↗ alpha bundles › Long alpha-hairpin › DUF683 › DUF683 › Med10 0.70 54.0 4.61e-01 85.5% 52.9%
5027676 101.35.1.0 ↗ alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX 0.70 55.0 5.51e-01 94.5% 87.3%
3839497 150.5.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › ESAT-6 like › ESAT-6 like 0.68 55.0 4.66e-01 85.5% 56.5%
3641527 192.8.1.353 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › Med10 0.68 53.0 4.67e-01 87.3% 57.5%
4116112 192.8.1.353 ↗ alpha bundles › Long alpha-hairpin › Eukaryotic DNA topoisomerase I, dispensable insert domain › Eukaryotic DNA topoisomerase I, dispensable insert domain › Med10 0.67 51.0 4.48e-01 87.3% 56.2%
4572664 604.3.1.0 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.66 48.0 4.40e-01 85.5% 60.0%
4963338 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.64 48.0 4.71e-01 85.5% 73.3%
5005528 604.5.1.2 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › PhoU 0.63 53.0 4.37e-01 94.5% 88.0%
3513072 323.1.1.6 ↗ a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › Carn_acyltransf 0.61 51.0 3.43e-01 92.7% 25.6%
5078401 2004.5.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › Differentially expressed in normal cells and neoplasia (DENN) domain › Differentially expressed in normal cells and neoplasia (DENN) domain 0.60 45.0 3.20e-01 87.3% 88.7%