Back to structures

ON453896.1__WAK79104.1__X__00042

Bact-Vir

ON453896.1__WAK79104.1__X__00042

Identity

Accession:
ON453896 ↗
Kingdom:
phage

Quality

89.1 mean pLDDT

Taxonomy

TaxID: 2951968

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 4-78
PDB
Domain cluster: representative
CATH (38)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3ezjA02 3.30.1370.120 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.70 48.0 4.95e-01 100.0% 77.9%
3ossD00 3.30.1370.120 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.69 46.0 3.62e-01 96.0% 32.5%
4e9jB01 3.30.1370.120 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.65 42.0 3.44e-01 92.0% 35.5%
1s28A00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.63 46.0 3.87e-01 100.0% 45.4%
4py5A01 3.30.310.10 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › TATA-Binding Protein 0.63 49.0 5.06e-01 100.0% 90.3%
4e9jA02 3.30.1370.120 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.63 44.0 4.54e-01 90.7% 79.7%
5cwaA00 3.60.120.10 Alpha Beta › 4-Layer Sandwich › Anthranilate synthase › Anthranilate synthase 0.63 53.0 3.27e-01 97.3% 47.5%
1vx7H01 3.90.930.12 Alpha Beta › Alpha-Beta Complex › Outer Surface Protein A; domain 3 › Ribosomal protein L6 0.63 52.0 5.03e-01 100.0% 80.0%
4i8oA01 3.30.310.240 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Bacterial toxin RNase RnlA/LsoA, N-terminal domain 0.62 53.0 5.01e-01 94.7% 92.1%
6fijA02 3.40.366.10 Alpha Beta › 3-Layer(aba) Sandwich › Malonyl-Coenzyme A Acyl Carrier Protein; domain 2 › Malonyl-Coenzyme A Acyl Carrier Protein, domain 2 0.61 40.0 2.67e-01 90.7% 15.6%
3uoxB01 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.61 41.0 2.72e-01 80.0% 17.6%
5b7hB01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.60 50.0 4.49e-01 93.3% 83.3%
3i3vB01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.58 50.0 3.92e-01 98.7% 94.1%
3u1kB04 3.30.1370.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › K Homology domain, type 1 0.58 39.0 4.00e-01 90.7% 72.2%
1mzgB00 3.90.1010.10 Alpha Beta › Alpha-Beta Complex › Sufe protein. Chain: A › 0.58 45.0 3.64e-01 84.0% 96.5%
4limA00 3.90.920.10 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › DNA primase, PRIM domain 0.58 46.0 2.90e-01 100.0% 17.1%
3dfuA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.57 46.0 3.91e-01 90.7% 84.5%
3f6tA01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.57 42.0 3.45e-01 100.0% 41.2%
1ni7A00 3.90.1010.10 Alpha Beta › Alpha-Beta Complex › Sufe protein. Chain: A › 0.57 45.0 3.60e-01 86.7% 94.6%
5xuhA00 3.90.470.20 Alpha Beta › Alpha-Beta Complex › Ribosomal Protein L22; Chain A › 4'-phosphopantetheinyl transferase domain 0.56 41.0 3.55e-01 78.7% 84.0%
5ao2B02 3.30.70.2760 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.56 45.0 4.30e-01 90.7% 82.0%
3gwmA00 3.90.470.20 Alpha Beta › Alpha-Beta Complex › Ribosomal Protein L22; Chain A › 4'-phosphopantetheinyl transferase domain 0.56 43.0 3.62e-01 84.0% 84.5%
2wdoA00 3.90.470.20 Alpha Beta › Alpha-Beta Complex › Ribosomal Protein L22; Chain A › 4'-phosphopantetheinyl transferase domain 0.55 42.0 3.61e-01 82.7% 82.1%
2im5A00 3.20.140.10 Alpha Beta › Alpha-Beta Barrel › nicotinate phosphoribosyltransferase › nicotinate phosphoribosyltransferase 0.55 48.0 3.09e-01 100.0% 23.7%
3p34A02 3.30.1120.30 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › POLO box domain 0.55 44.0 4.07e-01 98.7% 68.0%
1yirA00 3.20.140.10 Alpha Beta › Alpha-Beta Barrel › nicotinate phosphoribosyltransferase › nicotinate phosphoribosyltransferase 0.55 47.0 3.03e-01 100.0% 22.8%
2gb3A01 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.55 41.0 3.32e-01 96.0% 40.0%
4hstA01 1.10.439.10 Mainly Alpha › Orthogonal Bundle › Penicillin Amidohydrolase; domain 1 › Penicillin Amidohydrolase, domain 1 0.54 46.0 3.66e-01 94.7% 80.8%
2bddA00 3.90.470.20 Alpha Beta › Alpha-Beta Complex › Ribosomal Protein L22; Chain A › 4'-phosphopantetheinyl transferase domain 0.54 39.0 3.34e-01 78.7% 80.3%
5xukA00 3.90.470.20 Alpha Beta › Alpha-Beta Complex › Ribosomal Protein L22; Chain A › 4'-phosphopantetheinyl transferase domain 0.53 40.0 3.56e-01 82.7% 86.1%
2p92A00 3.30.70.1490 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Cysteine protease Prp 0.53 47.0 4.41e-01 100.0% 92.6%
5cq2A02 2.20.70.10 Mainly Beta › Single Sheet › Ubiquitin Ligase Nedd4; Chain: W; › 0.53 31.0 3.67e-01 82.7% 97.7%
2rc8A01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.52 46.0 3.55e-01 100.0% 54.9%
2bhoA00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.52 44.0 3.89e-01 93.3% 81.8%
1e6vB02 1.20.840.10 Mainly Alpha › Up-down Bundle › Methyl-coenzyme M Reductase; Chain B, domain 2 › Methyl-coenzyme M reductase, alpha/beta subunit, C-terminal 0.51 44.0 3.05e-01 100.0% 92.4%
1hbxA01 3.40.1810.10 Alpha Beta › 3-Layer(aba) Sandwich › SRF-like › Transcription factor, MADS-box 0.51 36.0 3.68e-01 78.7% 78.9%
3cjnA00 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 0.51 44.0 3.56e-01 97.3% 69.2%
1t3aA00 3.90.1240.10 Alpha Beta › Alpha-Beta Complex › Zincin-like › "Metalloproteases (""zincins""), catalytic domain like" 0.51 44.0 2.83e-01 100.0% 42.5%
ECOD (25)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3329738 327.11.2.0 a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) 0.65 50.0 4.88e-01 100.0% 75.3%
3420946 327.11.2.0 a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) 0.64 48.0 4.83e-01 94.7% 80.0%
3739949 306.6.1.0 a+b two layers › Glucose permease domain IIB-like › PH0987 N-terminal domain-like › PH0987 N-terminal domain-like 0.63 46.0 4.43e-01 100.0% 68.2%
3598177 318.1.1.0 a+b two layers › Ribosomal protein L6 › Ribosomal protein L6 › Ribosomal protein L6 0.62 51.0 4.92e-01 100.0% 80.0%
3693017 304.48.1.0 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.61 39.0 2.57e-01 96.0% 13.2%
3209439 304.48.1.0 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.61 42.0 2.80e-01 96.0% 16.9%
4029258 327.11.2.1 a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › KH_1 0.60 44.0 4.54e-01 97.3% 85.7%
3521093 3532.1.1.1 alpha arrays › RNA-binding domain of telomerase › RNA-binding domain of telomerase › RNA-binding domain of telomerase › Telomerase_RBD 0.59 51.0 3.55e-01 100.0% 86.9%
4349515 304.11.1.0 a+b two layers › Alpha-beta plaits › Probable ACP-binding domain of malonyl-CoA ACP transacylase › Probable ACP-binding domain of malonyl-CoA ACP transacylase 0.58 38.0 3.96e-01 90.7% 72.9%
3714022 304.24.1.3 a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › EFG_III 0.57 39.0 4.20e-01 89.3% 88.3%
6733 244.3.1.2 a+b two layers › FAD-linked reductases, C-terminal domain-like › SufE/NifU › SufE/NifU › SufE 0.57 45.0 3.60e-01 86.7% 94.6%
3281747 213.5.1.1 a+b three layers › Nat/Ivy › AlkZ C-terminal domain › AlkZ C-terminal domain › AlkZ-like 0.56 44.0 4.06e-01 90.7% 82.9%
3966747 325.1.4.3 a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Nicotinate/Quinolinate PRTase N-terminal domain-like › NAPRTase_N 0.54 47.0 3.87e-01 100.0% 61.4%
4355414 301.8.1.1 a+b three layers › Bacillus chorismate mutase-like › 4'-phosphopantetheinyl transferase › 4'-phosphopantetheinyl transferase › ACPS 0.54 41.0 3.49e-01 82.7% 86.2%
4681401 301.8.1.1 a+b three layers › Bacillus chorismate mutase-like › 4'-phosphopantetheinyl transferase › 4'-phosphopantetheinyl transferase › ACPS 0.54 40.0 3.58e-01 82.7% 87.0%
4493048 301.8.1.1 a+b three layers › Bacillus chorismate mutase-like › 4'-phosphopantetheinyl transferase › 4'-phosphopantetheinyl transferase › ACPS 0.53 41.0 3.51e-01 84.0% 77.6%
4426878 2003.1.2.49 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › FAD_binding_2+FAD_binding_3 0.53 45.0 3.03e-01 93.3% 73.9%
4968843 131.1.1.3 alpha complex topology › PDEase-like › HD-domain/PDEase-like › HD-domain/PDEase-like › HD 0.53 45.0 2.98e-01 98.7% 52.7%
3194913 7579.1.1.1 a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › COesterase 0.53 45.0 2.66e-01 97.3% 49.6%
3195256 327.16.1.0 a+b two layers › Alpha-lytic protease prodomain-like › Ring-building motif II in type III secretion system › Ring-building motif II in type III secretion system 0.53 44.0 4.29e-01 100.0% 84.7%
3256843 220.1.1.8 beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.52 43.0 3.90e-01 92.0% 81.9%
3216300 2002.1.1.30 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Glyco_hydro_18 0.52 44.0 2.85e-01 93.3% 31.8%
3259128 220.1.1.8 beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.52 41.0 3.51e-01 88.0% 90.4%
3263649 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.51 42.0 3.54e-01 90.7% 86.9%
5035757 1036.1.1.1 a+b two layers › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › 60S ribosomal export protein NMD3 a+b domain › NMD3 0.51 36.0 3.33e-01 90.7% 55.2%
D2 high residues 110-362
PDB
CATH (10)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4i68A00 3.30.70.1800 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.67 24.0 3.95e-01 86.2% 88.9%
2atzA00 3.90.920.20 Alpha Beta › Alpha-Beta Complex › DNA primase, PRIM domain › HP0184-like 0.65 44.0 5.26e-01 86.6% 98.9%
1z1dB00 3.40.1310.20 Alpha Beta › 3-Layer(aba) Sandwich › Replication Protein E1; Chain: A, › 0.64 30.0 4.10e-01 75.1% 84.7%
2efpA02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.56 23.0 3.54e-01 78.7% 93.9%
2ia0B02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.56 24.0 3.70e-01 80.6% 100.0%
3e3xA02 3.30.70.240 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.55 22.0 3.48e-01 81.0% 94.7%
4m1xD00 3.30.1360.240 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.55 17.0 2.99e-01 96.4% 87.5%
1r89A03 3.30.70.590 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Poly(A) polymerase predicted RNA binding domain 0.54 29.0 3.86e-01 85.4% 97.8%
1b24A01 3.10.28.10 Alpha Beta › Roll › Endonuclease I-creI › Homing endonucleases 0.50 20.0 3.15e-01 75.5% 93.7%
2h5eA03 3.30.70.3280 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Peptide chain release factor 3, domain III 0.50 25.0 3.33e-01 73.9% 86.9%
ECOD (21)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
185296 862.1.1.4 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › RepB_primase 0.79 53.0 5.95e-01 86.6% 85.9%
4394681 862.1.1.4 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain › RepB_primase 0.72 52.0 5.79e-01 85.8% 90.2%
4173219 304.8.1.1 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › Thr_dehydrat_C 0.64 24.0 4.09e-01 70.4% 97.8%
5047086 304.24.1.0 a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.63 23.0 3.67e-01 80.2% 85.3%
5046352 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.63 25.0 3.78e-01 81.0% 85.7%
143128 304.55.1.4 a+b two layers › Alpha-beta plaits › Origin of replication-binding domains › Origin of replication-binding domains › T_Ag_DNA_bind 0.62 29.0 4.10e-01 75.1% 92.4%
3356352 390.1.1.0 few secondary structure elements › Hairpin loop containing domain-like › Hairpin loop containing domain-like › Hairpin loop containing domain-like 0.61 22.0 3.76e-01 96.0% 98.8%
3598810 862.1.1.0 a+b complex topology › Prim-pol domain › Prim-pol domain › Prim-pol domain 0.60 36.0 4.24e-01 82.2% 82.2%
3295535 390.1.1.6 few secondary structure elements › Hairpin loop containing domain-like › Hairpin loop containing domain-like › Hairpin loop containing domain-like › PAN_2 0.60 22.0 3.66e-01 96.0% 94.1%
3565650 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.60 23.0 3.80e-01 72.7% 97.8%
3662913 390.1.1.6 few secondary structure elements › Hairpin loop containing domain-like › Hairpin loop containing domain-like › Hairpin loop containing domain-like › PAN_2 0.57 22.0 3.08e-01 96.4% 67.7%
5045299 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.56 21.0 2.87e-01 79.8% 61.5%
5072361 304.4.1.1 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel › AsnC_trans_reg 0.56 23.0 3.68e-01 74.7% 100.0%
5047232 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.54 22.0 3.42e-01 81.4% 94.0%
5045792 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.53 25.0 3.61e-01 82.6% 96.5%
5044656 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.52 26.0 3.65e-01 82.6% 96.0%
4142391 304.48.1.0 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like 0.51 25.0 3.27e-01 75.5% 83.7%
4943756 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.51 25.0 3.54e-01 82.2% 98.3%
4979169 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.51 24.0 3.46e-01 81.0% 99.1%
4973396 304.4.1.0 a+b two layers › Alpha-beta plaits › Dimeric alpha+beta barrel › Dimeric alpha+beta barrel 0.51 33.0 3.89e-01 71.5% 91.7%
3732227 304.110.1.0 a+b two layers › Alpha-beta plaits › Acylphosphatase-like › Acylphosphatase-like 0.51 23.0 3.07e-01 82.2% 79.2%