←Back to structures

MG948468.1__AVJ51772.1__Vid5_gp17__00017

Bact-Vir

MG948468.1__AVJ51772.1__Vid5_gp17__00017

Identity

Accession:
MG948468 ↗
Kingdom:
phage

Quality

88.5 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Vidquintavirus› Pantoea_phage_vB_PagS_Vid5

TaxID: 2099652

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 39-109
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF23812.2 best Phage_TAC_18 46.0 6.20e-12 77.5% 76.2%
CATH (27)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3favD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.76 56.0 5.47e-01 77.5% 78.2%
2ozbB01 1.10.287.4070 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.75 63.0 5.09e-01 91.5% 77.9%
3na7A00 1.10.287.1490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.74 55.0 3.70e-01 78.9% 23.2%
2ox6D00 1.10.3100.10 Mainly Alpha › Orthogonal Bundle › Putative cytoplasmic protein › Putative cytoplasmic protein 0.73 53.0 3.95e-01 74.6% 39.1%
2hszA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.72 52.0 5.18e-01 76.1% 82.7%
1zx3A01 1.10.287.1020 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › NE0241-like 0.72 42.0 3.95e-01 76.1% 49.4%
2kp8A00 1.20.5.170 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.71 54.0 5.46e-01 80.3% 86.1%
5h20A00 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 0.69 50.0 4.50e-01 78.9% 77.7%
1wdzA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.68 52.0 3.56e-01 80.3% 26.0%
1st6A03 1.20.120.810 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Vinculin, Vh2 four-helix bundle 0.67 49.0 3.42e-01 77.5% 44.5%
2qmaA01 1.20.1650.10 Mainly Alpha › Up-down Bundle › PLP-dependent transferase-like › PLP-dependent transferases 0.66 38.0 3.53e-01 100.0% 46.5%
1g2rA00 3.30.1230.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Cytosolic Protein; Chain: A; › YlxR-like 0.66 49.0 4.53e-01 80.3% 68.1%
1a41A02 1.20.120.380 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Type 1-topoisomerase catalytic fragment, domain 2 0.65 49.0 4.51e-01 81.7% 76.6%
5iwuA02 3.90.1200.10 Alpha Beta › Alpha-Beta Complex › Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 › Aminoglycoside phosphotransferase (APH), C-terminal lobe 0.64 52.0 3.82e-01 90.1% 68.0%
1t6sA01 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 0.64 47.0 4.49e-01 78.9% 66.3%
1zkeA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.64 51.0 4.91e-01 94.4% 75.3%
1rv2D04 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.63 44.0 4.49e-01 84.5% 74.3%
3rimB01 3.40.50.970 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Thiamin diphosphate (ThDP)-binding fold, Pyr/PP domains 0.63 55.0 3.51e-01 98.6% 94.5%
3a1kA01 1.10.20.60 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Glu-tRNAGln amidotransferase C subunit, N-terminal domain 0.62 43.0 4.64e-01 74.6% 96.3%
2vxdA00 1.10.10.2100 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Nucleophosmin, C-terminal domain 0.61 41.0 4.57e-01 70.4% 98.1%
2hoqA02 1.10.150.520 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.59 44.0 4.25e-01 80.3% 79.7%
8d7hD01 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.58 49.0 3.62e-01 90.1% 84.4%
3rrcB01 1.20.1310.20 Mainly Alpha › Up-down Bundle › 5 helical Cullin repeat like › Duffy-antigen binding domain 0.58 47.0 3.65e-01 90.1% 63.9%
1uujA00 1.20.960.30 Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A › 0.56 41.0 4.07e-01 80.3% 77.6%
1knzA01 6.10.280.20 Special › Helix non-globular › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Rotavirus non-structural protein NSP3, N-terminal domain 0.53 37.0 3.31e-01 73.2% 74.5%
7wd3A02 1.10.8.60 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.52 42.0 4.04e-01 88.7% 75.6%
3dxiA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.52 42.0 2.88e-01 94.4% 62.9%
ECOD (32)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4613072 101.1.2.721 ↗ alpha arrays › HTH › HTH › winged helix domain › MarR_2, PF27113 0.84 53.0 3.92e-01 88.7% 27.9%
5035232 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.81 56.0 5.65e-01 85.9% 71.4%
3725506 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 0.81 57.0 4.83e-01 85.9% 47.3%
5002748 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.81 56.0 5.55e-01 87.3% 68.0%
5050359 605.1.1.1 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA 0.77 54.0 5.46e-01 81.7% 72.9%
5020685 7516.1.1.2 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glycos_transf_2 0.74 54.0 3.44e-01 85.9% 17.2%
3232923 3291.1.1.221 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Nnf1 0.73 53.0 4.09e-01 76.1% 34.8%
3718035 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.73 47.0 4.94e-01 88.7% 72.3%
3889810 4177.1.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.73 54.0 3.75e-01 78.9% 28.5%
4457830 589.1.1.2 ↗ alpha arrays › Triger factor/SurA peptide-binding domain-like › Triger factor/SurA peptide-binding domain-like › Porin chaperone SurA, peptide-binding domain › SurA_N_3 0.73 50.0 3.53e-01 70.4% 27.7%
3723759 3755.4.1.0 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.72 55.0 3.97e-01 78.9% 95.0%
3881313 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.71 49.0 5.07e-01 71.8% 80.0%
3337263 198.1.1.0 ↗ alpha arrays › Saposin-like › Saposin-like › Saposin-like 0.70 58.0 5.36e-01 90.1% 75.6%
4999868 604.1.1.264 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Oxidored_q2 0.69 51.0 4.70e-01 77.5% 88.9%
5017062 7094.1.1.4 ↗ alpha bundles › Paddle domain of mitochondrial dynamin › Paddle domain of mitochondrial dynamin › Paddle domain of mitochondrial dynamin › PF27273 0.69 50.0 4.93e-01 91.5% 72.0%
4306568 4207.1.2.1 ↗ alpha duplicates or obligate multimers › Mediator hinge subcomplex-like › Mediator hinge subcomplex-like › MED7 hinge region › Med7 0.69 51.0 4.26e-01 78.9% 47.8%
4177674 4992.1.1.23 ↗ extended segments › RelB-like › RelB-like › RelB-like › Seryl_tRNA_N 0.68 50.0 4.29e-01 88.7% 50.0%
4247116 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.68 49.0 4.24e-01 88.7% 49.1%
3282600 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.66 58.0 3.69e-01 94.4% 45.3%
3840952 601.19.1.39 ↗ alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein › LIN9_C 0.66 49.0 4.84e-01 78.9% 77.3%
4996029 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.65 50.0 3.22e-01 83.1% 19.1%
3477418 4992.1.1.12 ↗ extended segments › RelB-like › RelB-like › RelB-like › LIN9_C 0.65 49.0 4.39e-01 78.9% 61.1%
3365397 4982.1.1.3 ↗ alpha arrays › KaiA/RbsU domain-like › KaiA/RbsU domain › KaiA/RbsU domain › Tic110 0.64 54.0 4.69e-01 94.4% 69.1%
3747266 101.1.10.1 ↗ alpha arrays › HTH › HTH › Cyclin-like › Cyclin_N 0.63 47.0 3.50e-01 83.1% 34.5%
4653130 101.1.2.20 ↗ alpha arrays › HTH › HTH › winged helix domain › Arg_repressor 0.62 44.0 4.09e-01 76.1% 76.8%
2485668 7025.1.1.2 ↗ alpha bundles › LIN9-LIN52 heterodimer › LIN9-LIN52 heterodimer › LIN9-LIN52 heterodimer › LIN9_C 0.62 44.0 4.20e-01 87.3% 64.3%
3927159 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.61 54.0 4.36e-01 100.0% 77.9%
4127805 101.1.2.25 ↗ alpha arrays › HTH › HTH › winged helix domain › FUR 0.61 50.0 4.03e-01 95.8% 69.3%
3992404 190.1.1.1 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.58 46.0 4.35e-01 84.5% 76.5%
3496552 190.1.1.3 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box_2 0.57 42.0 3.90e-01 77.5% 68.9%
4015915 190.1.1.3 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box_2 0.56 43.0 4.10e-01 80.3% 87.5%
4291633 4205.1.1.0 ↗ a+b two layers › SMI1/KNR4-like › SMI1/KNR4-like › SMI1/KNR4-like 0.54 37.0 2.91e-01 71.8% 53.9%