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NC_042063.1__YP_009617896.1__QII00_sBgp03__00003

Bact-Vir

NC_042063.1__YP_009617896.1__QII00_sBgp03__00003

Identity

Accession:
NC_042063 ↗
Kingdom:
phage

Quality

64.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Nonanavirus› Salmonella_phage_SP069

TaxID: 1173760

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 177-250
PDB
Domain cluster: representative
CATH (31)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ywmA02 1.20.1270.150 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Surface Active Protein 0.68 53.0 5.26e-01 82.4% 84.2%
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 51.0 3.60e-01 81.1% 81.0%
2zxqA06 1.20.1270.70 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Designed single chain three-helix bundle 0.67 52.0 5.49e-01 83.8% 93.9%
2h56A02 1.10.340.30 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Hypothetical protein; domain 2 0.66 46.0 4.04e-01 73.0% 88.6%
1lq7A00 1.20.1270.70 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Designed single chain three-helix bundle 0.66 49.0 5.15e-01 79.7% 91.0%
2icwG01 1.20.120.390 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hla class ii histocompatibility antigen, dr alpha chain. Chain D, domain 1 0.65 57.0 4.88e-01 100.0% 74.2%
2g8lB01 1.10.8.380 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Uncharacterised protein PF01937, DUF89, domain 1 0.64 48.0 5.00e-01 81.1% 98.5%
1qdbA02 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.64 49.0 3.89e-01 81.1% 55.9%
3dfzA02 1.10.8.610 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › SirC, precorrin-2 dehydrogenase, C-terminal helical domain-like 0.64 46.0 4.63e-01 82.4% 77.0%
2oezA02 1.10.3900.10 Mainly Alpha › Orthogonal Bundle › YacF-like › YacF-like 0.63 46.0 3.56e-01 77.0% 68.7%
6wh0A01 1.10.437.10 Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › Blc2-like 0.63 55.0 4.30e-01 95.9% 78.3%
4bemJ00 1.20.120.610 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › lithium bound rotor ring of v- atpase 0.62 53.0 4.12e-01 100.0% 65.7%
1zylA03 1.20.1270.170 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.62 53.0 4.82e-01 100.0% 98.1%
6p73A02 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.61 46.0 3.82e-01 83.8% 55.9%
3d1uA03 1.20.1270.240 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.60 52.0 4.76e-01 100.0% 76.2%
4uobA02 1.10.340.30 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Hypothetical protein; domain 2 0.59 43.0 3.66e-01 78.4% 88.1%
3dtoA01 1.10.472.50 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › HD-domain/PDEase-like 0.58 49.0 4.66e-01 91.9% 97.7%
5grqA00 1.10.8.810 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Daxx helical bundle domain 0.58 49.0 4.67e-01 100.0% 81.1%
1tdpA00 1.20.1440.50 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Ta0600-like 0.58 43.0 3.82e-01 81.1% 54.1%
1ohuA00 1.10.437.10 Mainly Alpha › Orthogonal Bundle › Apoptosis Regulator Bcl-x › Blc2-like 0.58 49.0 3.82e-01 95.9% 70.3%
2hoqA02 1.10.150.520 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 0.56 41.0 4.03e-01 77.0% 82.3%
2zopA00 1.10.520.30 Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › AF1862-like domain 0.56 42.0 3.69e-01 81.1% 59.8%
2b8iA00 1.20.1280.100 Mainly Alpha › Up-down Bundle › Monooxygenase › Pas factor, saposin domain 0.55 40.0 4.01e-01 78.4% 92.2%
6l3tA01 1.20.1440.80 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › Gap junction channel protein cysteine-rich domain 0.55 41.0 3.16e-01 85.1% 62.8%
4fm3A00 1.20.1270.390 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.55 40.0 3.76e-01 81.1% 68.4%
1xl7A01 1.10.275.20 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Choline/Carnitine o-acyltransferase 0.54 40.0 3.63e-01 79.7% 81.6%
2bg1A01 3.90.1310.40 Alpha Beta › Alpha-Beta Complex › Penicillin-binding protein 2a (Domain 2) › 0.53 38.0 3.78e-01 75.7% 94.8%
1or7B01 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.52 41.0 3.81e-01 86.5% 96.8%
3ed5A02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.52 36.0 3.47e-01 73.0% 67.9%
2id6A02 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.51 43.0 3.42e-01 93.2% 87.0%
2ra1A03 1.20.58.770 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.51 38.0 4.11e-01 81.1% 93.7%
ECOD (33)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5048050 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.70 52.0 3.50e-01 81.1% 39.6%
5074726 633.10.1.0 ↗ alpha bundles › Bromodomain-like › IVS-encoded protein-like › IVS-encoded protein-like 0.66 48.0 4.63e-01 77.0% 67.1%
3240158 3525.1.1.0 ↗ alpha arrays › Bromodomain-containing protein 4 ET domain › Bromodomain-containing protein 4 ET domain › Bromodomain-containing protein 4 ET domain 0.66 59.0 5.52e-01 100.0% 94.4%
4652715 3831.1.1.0 ↗ alpha bundles › Secreted protein of unknown function DUF1311 › Secreted protein of unknown function DUF1311 › Secreted protein of unknown function DUF1311 0.66 49.0 4.42e-01 81.1% 60.0%
4251730 6056.1.1.2 ↗ alpha arrays › SP1917-like › SP1917-like › SP1917-like › PrmC_N 0.65 55.0 5.62e-01 94.6% 100.0%
3406162 4006.1.1.13 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › DUF842 0.65 50.0 4.21e-01 83.8% 92.0%
5031356 142.1.1.0 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors 0.64 47.0 4.85e-01 78.4% 91.4%
3391955 611.10.1.0 ↗ alpha bundles › N-cbl like › DAXX helical bundle domain › DAXX helical bundle domain 0.63 55.0 5.40e-01 100.0% 95.0%
3479273 611.10.1.0 ↗ alpha bundles › N-cbl like › DAXX helical bundle domain › DAXX helical bundle domain 0.63 55.0 5.37e-01 100.0% 92.5%
3655820 611.9.1.4 ↗ alpha bundles › N-cbl like › Resistance protein (Rx) N-terminal domain › Resistance protein (Rx) N-terminal domain › Rx_N 0.63 54.0 4.40e-01 100.0% 91.3%
3431353 1128.1.1.10 ↗ alpha bundles › LYR protein › LYR protein › LYR protein › VIN3_C 0.63 52.0 5.33e-01 100.0% 98.6%
3181616 601.1.2.72 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › SesA 0.62 54.0 4.29e-01 98.6% 67.1%
3730940 3755.4.1.0 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.62 54.0 4.31e-01 100.0% 73.5%
3236976 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.62 45.0 3.63e-01 78.4% 42.7%
4982157 633.21.1.0 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 0.61 45.0 4.25e-01 78.4% 71.1%
3237264 3755.4.1.82 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Snf7 0.61 52.0 4.41e-01 98.6% 91.5%
3212939 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.60 43.0 3.49e-01 78.4% 43.9%
3241203 544.1.1.0 ↗ alpha bundles › Functional domain of the splicing factor Prp18 › Functional domain of the splicing factor Prp18 › Functional domain of the splicing factor Prp18 0.60 52.0 4.50e-01 100.0% 63.3%
2822545 101.1.8.3 ↗ alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › Topoisom_I,Topo_C_assoc 0.59 33.0 3.72e-01 71.6% 68.4%
3288182 5059.1.1.1 ↗ alpha bundles › Drug/Metabolite transporter › Drug/Metabolite transporter › Drug/Metabolite transporter › EamA 0.59 44.0 3.06e-01 82.4% 66.9%
2133274 611.10.1.1 ↗ alpha bundles › N-cbl like › DAXX helical bundle domain › DAXX helical bundle domain › Daxx 0.59 49.0 4.77e-01 100.0% 84.9%
3624530 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.57 42.0 3.37e-01 79.7% 43.1%
3209446 632.22.1.131 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats › SOG2 0.57 42.0 3.56e-01 81.1% 65.2%
5037158 7531.1.1.1 ↗ a/b three-layered sandwiches › Carbamate kinase-like › Carbamate kinase-like › Carbamate kinase-like › AA_kinase 0.57 49.0 3.31e-01 100.0% 48.5%
3664164 3922.1.1.0 ↗ alpha bundles › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 › Helical domain in structural maintenance of chromosomes protein 3 0.55 40.0 3.37e-01 77.0% 79.2%
3757390 604.5.1.31 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › TRAM_LAG1_CLN8 0.54 45.0 3.25e-01 100.0% 43.0%
4937843 2005.1.1.7 ↗ a/b three-layered sandwiches › HUP domain-like › HUP domains › HUP domains › tRNA-synt_1d 0.54 39.0 2.50e-01 77.0% 27.2%
3953824 628.1.1.1 ↗ alpha bundles › Fatty acid responsive transcription factor FadR, C-terminal domain › Fatty acid responsive transcription factor FadR, C-terminal domain › Fatty acid responsive transcription factor FadR, C-terminal domain › FCD 0.53 38.0 3.15e-01 74.3% 60.7%
3459613 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.53 38.0 3.11e-01 79.7% 67.3%
5039563 604.5.1.0 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) 0.52 45.0 3.38e-01 100.0% 62.9%
3716410 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.52 37.0 3.63e-01 78.4% 91.8%
3406484 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.50 36.0 3.08e-01 79.7% 62.9%
4957472 7516.1.1.2 ↗ a/b three-layered sandwiches › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Nucleotide-diphospho-sugar transferases › Glycos_transf_2 0.50 42.0 2.87e-01 100.0% 47.4%
D2 medium residues 65-132
PDB
Domain cluster: rep: MK373772.1__QBQ76654.1__PTXU04_00040__00040__D80-130
CATH (17)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2g29A01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.61 52.0 3.58e-01 98.5% 89.5%
4ua3A00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.59 52.0 3.83e-01 100.0% 68.3%
4iqyB00 3.40.220.10 Alpha Beta › 3-Layer(aba) Sandwich › Leucine Aminopeptidase, subunit E; domain 1 › Leucine Aminopeptidase, subunit E, domain 1 0.57 46.0 3.23e-01 88.2% 70.8%
3l5lA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.56 47.0 3.02e-01 97.1% 54.0%
1ryp100 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.56 45.0 3.17e-01 89.7% 36.9%
2f48A01 3.40.50.450 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.56 44.0 2.95e-01 88.2% 69.1%
4ku4A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.53 45.0 3.39e-01 94.1% 80.1%
3ih6E00 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.53 42.0 3.30e-01 97.1% 95.1%
4bqqB02 3.90.1750.20 Alpha Beta › Alpha-Beta Complex › Hect, E3 ligase catalytic domain fold › Putative Large Serine Recombinase; Chain B, Domain 2 0.53 39.0 2.91e-01 80.9% 41.1%
5ctnA00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.53 43.0 2.98e-01 89.7% 91.8%
3gy1B02 3.20.20.120 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Enolase-like C-terminal domain 0.51 43.0 2.93e-01 91.2% 36.1%
4pmxA00 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.51 45.0 2.95e-01 100.0% 61.8%
2f2hA02 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.51 44.0 2.78e-01 97.1% 40.2%
5unhA02 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.51 44.0 3.00e-01 100.0% 56.7%
1ak2A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 41.0 2.84e-01 86.8% 88.2%
2blfB01 1.10.760.10 Mainly Alpha › Orthogonal Bundle › Cytochrome Bc1 Complex; Chain D, domain 2 › Cytochrome c-like domain 0.50 32.0 3.36e-01 88.2% 68.3%
5e5bA01 3.40.350.10 Alpha Beta › 3-Layer(aba) Sandwich › Creatine Amidinohydrolase; Chain A, domain 1 › Creatinase/prolidase N-terminal domain 0.50 42.0 3.27e-01 100.0% 91.2%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3284380 304.128.1.0 ↗ a+b two layers › Alpha-beta plaits › ferredoxin-like domain in periplasmic region of MacB › ferredoxin-like domain in periplasmic region of MacB 0.60 40.0 4.02e-01 86.8% 67.1%
4989477 304.128.1.0 ↗ a+b two layers › Alpha-beta plaits › ferredoxin-like domain in periplasmic region of MacB › ferredoxin-like domain in periplasmic region of MacB 0.60 44.0 4.24e-01 86.8% 68.8%
4396869 244.1.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › FAD-linked reductases-C › FAD-linked reductases-C 0.58 46.0 4.08e-01 86.8% 73.0%
3627202 375.10.1.1 ↗ few secondary structure elements › Rubredoxin-like › Zinc finger domain of DNA polymerase-alpha › Zinc finger domain of DNA polymerase-alpha › zf-DNA_Pol 0.55 36.0 3.09e-01 70.6% 42.7%
2876662 375.10.1.1 ↗ few secondary structure elements › Rubredoxin-like › Zinc finger domain of DNA polymerase-alpha › Zinc finger domain of DNA polymerase-alpha › zf-DNA_Pol 0.54 36.0 3.00e-01 70.6% 40.3%
4826355 109.4.1.270 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › RYDR_Jsol 0.53 42.0 2.70e-01 88.2% 70.0%
3231096 5069.1.1.7 ↗ alpha bundles › Transmembrane heme-binding four-helical bundle › Transmembrane heme-binding four-helical bundle › Transmembrane di-heme cytochromes › Cytochrom_B561 0.52 43.0 2.97e-01 92.6% 71.4%
3688510 2002.1.1.119 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › CutC 0.52 45.0 3.17e-01 98.5% 48.4%
3838996 3016.1.1.0 ↗ a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases 0.50 42.0 3.65e-01 95.6% 61.8%