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MF787246.1__ATG86365.1__LpeD_80__00058

Bact-Vir

MF787246.1__ATG86365.1__LpeD_80__00058

Identity

Accession:
MF787246 ↗
Kingdom:
phage

Quality

88.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Herelleviridae› Elpedvirus› Lactobacillus_phage_LpeD

TaxID: 2041210

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 3-76
PDB
Domain cluster: rep: ON113175.1__UQT01149.1__QOFMPA_00026__00026__D3-75
CATH (20)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
6a97C01 3.30.500.10 Alpha Beta › 2-Layer Sandwich › Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1 › MHC class I-like antigen recognition-like 0.65 47.0 3.97e-01 100.0% 44.3%
3f8kA00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.64 49.0 4.13e-01 83.8% 69.5%
2a1vA00 3.90.1150.30 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › 0.62 48.0 3.95e-01 85.1% 72.5%
3g3sA01 3.40.630.110 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › GNAT acetyltransferase-like 0.60 40.0 3.44e-01 74.3% 43.1%
4py5A01 3.30.310.10 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › TATA-Binding Protein 0.60 44.0 4.47e-01 91.9% 81.9%
1zxuA00 2.40.160.200 Mainly Beta › Beta Barrel › Porin › LURP1-related 0.60 52.0 4.10e-01 100.0% 86.4%
2w7tA00 3.40.50.880 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Class I glutamine amidotransferase (GATase) domain 0.59 49.0 3.38e-01 93.2% 34.8%
3gvzA00 3.60.60.10 Alpha Beta › 4-Layer Sandwich › Penicillin V Acylase; Chain A › Penicillin V Acylase; Chain A 0.58 46.0 3.19e-01 86.5% 84.8%
3t4nA01 3.30.310.80 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Kinase associated domain 1, KA1 0.56 49.0 4.53e-01 100.0% 85.4%
2ediA01 3.10.110.10 Alpha Beta › Roll › Ubiquitin Conjugating Enzyme › Ubiquitin Conjugating Enzyme 0.54 44.0 3.47e-01 91.9% 60.0%
3upsA00 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.53 39.0 3.55e-01 97.3% 55.6%
2mhgA00 2.20.130.30 Mainly Beta › Single Sheet › S-adenosyl-L-methionine-dependent methyltransferases › Protein of unknown function DUF2782 0.53 38.0 3.79e-01 77.0% 73.3%
1qz8A01 2.40.10.250 Mainly Beta › Beta Barrel › Thrombin, subunit H › Replicase NSP9 0.53 44.0 3.93e-01 91.9% 98.1%
2nvmA00 3.30.310.110 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › XisI-like 0.51 41.0 3.77e-01 94.6% 83.7%
4mxtA00 2.50.20.10 Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › Lipoprotein localisation LolA/LolB/LppX 0.51 36.0 2.74e-01 74.3% 76.5%
2bkkA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.51 41.0 3.92e-01 94.6% 92.2%
5amhA00 2.170.150.20 Mainly Beta › Beta Complex › Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A › Peptide methionine sulfoxide reductase. 0.51 34.0 3.09e-01 70.3% 93.4%
6eufA01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.51 42.0 2.90e-01 98.6% 82.8%
1ntyA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.50 43.0 3.69e-01 98.6% 87.9%
3a8pB01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.50 43.0 3.79e-01 100.0% 95.7%
ECOD (19)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3589304 331.23.1.0 ↗ a+b two layers › TBP-like › Integrator IntS9/IntS11 C-terminal domain › Integrator IntS9/IntS11 C-terminal domain 0.83 76.0 7.59e-01 95.9% 98.7%
3721665 213.1.1.27 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_7 0.63 49.0 3.55e-01 86.5% 78.2%
3606087 213.1.1.0 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.59 50.0 3.63e-01 97.3% 55.1%
3477031 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.58 50.0 4.01e-01 93.2% 77.9%
4843435 211.1.1.0 ↗ a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase 0.58 35.0 3.56e-01 97.3% 57.9%
4033194 211.1.1.24 ↗ a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Ble-like_N 0.56 37.0 3.95e-01 93.2% 78.5%
3179764 241.11.1.3 ↗ a+b two layers › Type III secretory system chaperone-like › YjbR-like › YjbR-like › Luciferase 0.55 44.0 3.81e-01 87.8% 88.1%
3394227 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.55 45.0 3.07e-01 91.9% 31.0%
3929074 220.1.1.125 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_PLEKHM2 0.54 47.0 3.71e-01 94.6% 78.0%
3894031 330.1.1.6 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Staufen_C 0.53 42.0 4.01e-01 90.5% 72.9%
3931394 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.53 46.0 3.51e-01 97.3% 73.1%
3396124 708.1.2.0 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › Mss4-like 0.52 35.0 3.31e-01 70.3% 88.4%
3809735 64.1.1.16 ↗ beta meanders › WW domain-like › WW domain › WW domain › DUF7650 0.52 38.0 3.69e-01 78.4% 72.9%
3401989 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.52 46.0 3.61e-01 98.6% 67.1%
3592743 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.52 41.0 4.07e-01 89.2% 91.3%
3870832 206.1.1.71 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase, Kdo 0.51 41.0 2.79e-01 89.2% 51.8%
3628479 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.51 44.0 3.14e-01 100.0% 41.2%
3801480 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.51 43.0 3.48e-01 98.6% 71.6%
4935086 3504.3.1.1 ↗ beta barrels › MutM N-terminal domain-like › Fibrinogen binding protein N-terminal domain › Fibrinogen binding protein N-terminal domain › NFACT_N 0.50 37.0 2.98e-01 81.1% 45.2%
D2 high residues 82-145
PDB
Domain cluster: rep: NC_071083.1__YP_010683437.1__PQF09_gp43__00043__D112-175
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2arpF02 3.30.60.30 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.58 33.0 3.20e-01 100.0% 47.2%
4pofA03 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.51 33.0 3.62e-01 100.0% 84.0%
6aqgD02 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.51 41.0 2.69e-01 93.8% 74.6%
4ba0A03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.51 29.0 3.18e-01 100.0% 68.6%
2l89A00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.50 43.0 3.70e-01 100.0% 83.3%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3593768 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.54 40.0 3.61e-01 82.8% 100.0%
3513462 70.4.1.8 ↗ beta barrels › beta-clip › Head decoration protein D (gpD, major capsid protein D) › Head decoration protein D (gpD, major capsid protein D) › Phage_cement 0.52 37.0 3.79e-01 87.5% 80.0%