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HQ630627.1__AEH03754.1__X__00328

Bact-Vir

HQ630627.1__AEH03754.1__X__00328

Identity

Accession:
HQ630627 ↗
Kingdom:
phage

Quality

83.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Chimalliviridae› Miltoncavirus› Pseudomonas_phage_PhiPA3

TaxID: 998086

Cluster

View cluster (2 members)

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 medium residues 1-22_124-158
PDB
Domain cluster: representative
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2o18A00 3.10.520.10 Alpha Beta › Roll › T-fold › ApbE-like domains 0.67 57.0 3.64e-01 100.0% 57.7%
4ig1A00 3.10.520.10 Alpha Beta › Roll › T-fold › ApbE-like domains 0.66 57.0 3.55e-01 100.0% 54.6%
1vrmA01 3.10.520.10 Alpha Beta › Roll › T-fold › ApbE-like domains 0.63 52.0 3.67e-01 100.0% 34.6%
2uvaG01 1.20.1050.120 Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 › 0.63 53.0 4.13e-01 100.0% 66.2%
3cyjA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.61 52.0 4.14e-01 100.0% 59.8%
4p1mB01 3.30.160.880 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Cell division protein ZapA protomer, N-terminal domain 0.61 37.0 3.98e-01 70.2% 75.6%
2chrA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.60 50.0 3.99e-01 100.0% 60.6%
3o2iA00 3.30.70.2710 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 50.0 4.33e-01 100.0% 71.0%
2n3gA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.57 38.0 3.56e-01 71.9% 52.8%
2jl8102 3.30.160.850 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.57 41.0 4.41e-01 84.2% 100.0%
2i9yA00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.56 39.0 2.90e-01 75.4% 91.7%
4n01A01 3.40.50.1980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nitrogenase molybdenum iron protein domain 0.54 42.0 3.44e-01 89.5% 94.0%
4q05A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.54 43.0 2.76e-01 94.7% 69.4%
3dmgA02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.53 43.0 3.16e-01 100.0% 46.4%
4mtlA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.53 44.0 3.11e-01 100.0% 42.3%
4f0jA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.53 41.0 2.70e-01 94.7% 84.0%
4fwwA01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.53 39.0 2.39e-01 86.0% 51.6%
2kvtA00 3.30.730.30 Alpha Beta › 2-Layer Sandwich › GCC-box Binding Domain › YaiA protein 0.52 35.0 3.36e-01 73.7% 57.7%
1wloA00 3.90.1010.10 Alpha Beta › Alpha-Beta Complex › Sufe protein. Chain: A › 0.52 43.0 3.40e-01 100.0% 57.4%
2xzmE01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.51 34.0 2.75e-01 75.4% 34.5%
1fm2B01 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.51 41.0 2.80e-01 100.0% 32.1%
ECOD (29)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3612009 230.4.1.1 ↗ a+b two layers › T-fold › ApbE-like › ApbE-like › ApbE 0.67 58.0 3.99e-01 100.0% 89.5%
3598156 230.4.1.0 ↗ a+b two layers › T-fold › ApbE-like › ApbE-like 0.65 56.0 3.90e-01 100.0% 92.3%
3404842 2007.2.3.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.65 43.0 2.77e-01 70.2% 57.0%
3378740 109.4.1.1291 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, E_motif 0.62 42.0 2.29e-01 70.2% 8.7%
3943961 230.4.1.1 ↗ a+b two layers › T-fold › ApbE-like › ApbE-like › ApbE 0.61 51.0 3.69e-01 100.0% 91.4%
3834151 109.4.1.3495 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, PPR_long, E_motif, TPR_24 0.61 41.0 2.38e-01 70.2% 15.2%
3677917 109.3.1.320 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › DYW_deaminase 0.59 40.0 3.04e-01 70.2% 60.0%
3446121 109.4.1.3478 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_1, PPR_2, DYW_deaminase, Eplus_motif, E_motif, TPR_24 0.59 40.0 2.26e-01 70.2% 12.7%
3683857 109.4.1.1285 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, DYW_deaminase, Eplus_motif, E_motif 0.59 39.0 2.24e-01 70.2% 13.0%
3381254 109.4.1.2593 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_long, Eplus_motif 0.58 39.0 2.48e-01 70.2% 27.1%
3593482 2.1.1.135 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › DUF3592 0.58 43.0 3.70e-01 84.2% 79.0%
3830169 109.4.1.1383 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3, DYW_deaminase, Eplus_motif, E_motif 0.57 39.0 2.19e-01 71.9% 10.7%
3266079 2003.1.5.73 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_16 0.56 46.0 3.15e-01 100.0% 38.5%
3688295 221.1.1.73 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › RASSF8-10_RA 0.55 35.0 3.14e-01 75.4% 43.5%
4462824 2003.1.5.174 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › tRNA_U5-meth_tr, Methyltransf_15 0.54 46.0 2.88e-01 100.0% 23.6%
3617145 2003.1.5.73 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_16 0.54 44.0 3.13e-01 100.0% 40.9%
5054267 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.54 37.0 2.55e-01 84.2% 17.1%
3399749 2498.1.1.9 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › Peptidase_M1 0.54 44.0 2.92e-01 94.7% 30.4%
5036188 205.1.1.33 ↗ a+b two layers › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › 4Fe-4S ferredoxin › Fer4_10 0.54 45.0 3.97e-01 98.2% 75.6%
5078644 2003.1.5.46 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › MTS 0.53 44.0 3.15e-01 100.0% 42.4%
4992408 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.53 30.0 3.30e-01 80.7% 64.4%
1314126 857.1.1.1 ↗ a+b duplicates or obligate multimers › Cell division protein ZapA-like › Cell division protein ZapA-like › Cell division protein ZapA-like › ZapA 0.53 39.0 3.30e-01 84.2% 54.2%
3586911 101.1.9.0 ↗ alpha arrays › HTH › HTH › Putative DNA-binding domain 0.52 39.0 3.47e-01 87.7% 87.4%
3719211 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.51 31.0 3.22e-01 100.0% 63.6%
5010744 221.1.1.0 ↗ a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.51 39.0 3.75e-01 82.5% 72.3%
4024946 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.51 40.0 2.75e-01 98.2% 58.9%
5029930 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.51 43.0 3.69e-01 100.0% 80.0%
2774486 3281.1.1.1 ↗ alpha complex topology › Sodium/proton antiporter subunits-like › Sodium/proton antiporter subunits-like › NADH-quinone oxidoreductase subunit L (NuoL)-related › Proton_antipo_M 0.50 36.0 2.15e-01 82.5% 15.4%
4374416 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.50 41.0 2.38e-01 100.0% 8.5%
D2 medium residues 23-123
PDB
Domain cluster: rep: OR228460.1__WNV47689.1__X__00015__D24-119
CATH (16)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ealA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.69 38.0 3.53e-01 91.1% 42.5%
6e5bN00 3.60.20.10 Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain 0.65 59.0 4.68e-01 100.0% 57.3%
2z0qA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.58 30.0 2.77e-01 73.3% 38.3%
2dfkC02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.58 26.0 2.35e-01 73.3% 28.4%
2z0fA04 3.30.310.50 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Alpha-D-phosphohexomutase, C-terminal domain 0.57 34.0 3.39e-01 89.1% 57.8%
5hkeA01 3.60.60.10 Alpha Beta › 4-Layer Sandwich › Penicillin V Acylase; Chain A › Penicillin V Acylase; Chain A 0.57 48.0 3.48e-01 95.0% 100.0%
3hl6A01 3.30.1300.50 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › Putative mobile pathogenicity island, N-terminal domain 0.57 35.0 3.99e-01 94.1% 85.1%
6yiiA01 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.56 43.0 3.37e-01 84.2% 74.8%
4nkbA01 3.30.1120.120 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.55 37.0 3.56e-01 96.0% 60.5%
1p6pA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.53 36.0 3.40e-01 90.1% 56.8%
1ib8A02 2.30.30.180 Mainly Beta › Roll › SH3 type barrels. › Ribosome maturation factor RimP, C-terminal domain 0.53 31.0 3.67e-01 77.2% 86.6%
1lfoA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.52 36.0 3.39e-01 91.1% 57.5%
3u83A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 34.0 3.46e-01 72.3% 68.3%
4bfiB02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 34.0 3.57e-01 72.3% 77.8%
3dasA00 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.50 43.0 3.12e-01 100.0% 83.8%
4clfA02 3.30.70.1230 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Nucleotide cyclase, GGDEF domain 0.50 39.0 3.28e-01 85.1% 91.8%
ECOD (12)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3567966 9.1.1.1 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › Lipocalin 0.64 38.0 3.89e-01 91.1% 61.1%
3386077 2.4.1.0 ↗ beta barrels › OB-fold › MOP-like › MOP-like 0.63 27.0 3.92e-01 70.3% 91.1%
5047706 210.1.2.4 ↗ a+b four layers › Ntn/PP2C › Ntn › Penicillin acylase, catalytic domain › AAT 0.62 56.0 4.12e-01 100.0% 62.6%
4147605 210.1.3.5 ↗ a+b four layers › Ntn/PP2C › Ntn › Class II glutamine amidotransferases › GATase_7 0.58 51.0 3.87e-01 100.0% 87.6%
3508839 298.1.1.24 ↗ a+b two layers › FwdE/GAPDH domain-like › Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain › Glyceraldehyde-3-phosphate dehydrogenase-like, C-terminal domain › GFO_IDH_MocA_C3 0.56 45.0 3.37e-01 83.2% 60.0%
3512735 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.52 37.0 2.86e-01 73.3% 70.7%
3264236 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.52 39.0 3.93e-01 87.1% 79.0%
3995797 220.1.1.160 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_MADD 0.52 31.0 3.77e-01 87.1% 92.3%
4034521 220.1.1.87 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › bPH_3 0.52 39.0 3.99e-01 88.1% 81.0%
4527067 206.1.3.40 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › ATPgrasp_YheCD 0.52 36.0 2.69e-01 100.0% 28.6%
3601994 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.50 37.0 3.14e-01 86.1% 47.6%
3251867 227.1.1.11 ↗ a+b two layers › DNA clamp › DNA clamp › DNA clamp › Hus1 0.50 38.0 3.48e-01 79.2% 98.5%