←Back to structures

LC768487.1__BEH88345.1__X__00057

Bact-Vir

LC768487.1__BEH88345.1__X__00057

Identity

Accession:
LC768487 ↗
Kingdom:
phage

Quality

81.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Alcyoneusvirus› Klebsiella_phage_phiKp_21

TaxID: 2979978

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 10-114
PDB
Domain cluster: rep: OM868075.1__UPT53026.1__X__00089__D7-115
D2 high residues 137-205
PDB
Domain cluster: representative
CATH (21)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1gccA00 3.30.730.10 Alpha Beta › 2-Layer Sandwich › GCC-box Binding Domain › AP2/ERF domain 0.87 63.0 6.62e-01 75.4% 88.9%
7wq5A01 3.30.730.10 Alpha Beta › 2-Layer Sandwich › GCC-box Binding Domain › AP2/ERF domain 0.84 63.0 6.86e-01 78.3% 100.0%
3nyiA02 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.68 50.0 4.00e-01 76.8% 68.6%
3bexA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.68 47.0 3.99e-01 72.5% 92.0%
1pzxA03 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.67 48.0 3.98e-01 75.4% 66.4%
1dt9A02 3.30.420.60 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 0.61 42.0 3.61e-01 72.5% 67.9%
4akgA14 1.20.1280.160 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.58 41.0 3.58e-01 75.4% 84.4%
2lkoA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.58 40.0 3.29e-01 73.9% 43.5%
3hi0A02 3.30.420.150 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Exopolyphosphatase. Domain 2 0.57 41.0 3.08e-01 76.8% 76.0%
3e9lA02 1.20.80.40 Mainly Alpha › Up-down Bundle › Acyl-CoA Binding Protein › Prp8 RNase H domain, fingers region 0.56 38.0 3.45e-01 71.0% 77.9%
4fp4A00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.55 44.0 3.17e-01 94.2% 81.1%
2qkdA04 2.60.120.1040 Mainly Beta › Sandwich › Jelly Rolls › ZPR1, A/B domain 0.54 37.0 3.07e-01 72.5% 68.5%
4qqwA01 1.10.3210.30 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › 0.54 40.0 2.84e-01 84.1% 80.1%
5hn3A00 3.40.718.10 Alpha Beta › 3-Layer(aba) Sandwich › Isopropylmalate Dehydrogenase › Isopropylmalate Dehydrogenase 0.54 39.0 2.51e-01 78.3% 83.4%
5h8yD02 3.30.413.10 Alpha Beta › 2-Layer Sandwich › Sulfite Reductase Hemoprotein; domain 1 › Sulfite Reductase Hemoprotein, domain 1 0.53 43.0 3.11e-01 89.9% 45.3%
2g47A03 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.53 39.0 2.78e-01 81.2% 26.9%
4uapA00 2.60.120.260 Mainly Beta › Sandwich › Jelly Rolls › Galactose-binding domain-like 0.52 36.0 2.82e-01 72.5% 64.7%
1v4eA00 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.51 41.0 2.86e-01 95.7% 77.1%
1yx1A00 3.20.20.150 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Divalent-metal-dependent TIM barrel enzymes 0.50 37.0 2.56e-01 79.7% 97.6%
1ckmA01 3.30.470.30 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › DNA ligase/mRNA capping enzyme 0.50 40.0 3.25e-01 95.7% 60.6%
1qmgB01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.50 35.0 2.56e-01 75.4% 81.9%
ECOD (35)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3380188 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.88 64.0 7.13e-01 75.4% 100.0%
3468885 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.86 64.0 6.06e-01 78.3% 73.8%
3467141 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.85 80.0 6.66e-01 100.0% 71.8%
3293480 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.81 66.0 6.83e-01 92.8% 90.8%
3440839 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.78 72.0 6.31e-01 100.0% 85.0%
3651077 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.78 65.0 6.51e-01 89.9% 100.0%
3370971 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.78 70.0 6.35e-01 97.1% 92.2%
3827127 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.77 70.0 6.21e-01 97.1% 80.0%
3299337 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.77 71.0 6.21e-01 98.6% 85.7%
3331331 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.77 70.0 6.10e-01 97.1% 76.0%
3333577 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.77 70.0 6.24e-01 98.6% 84.2%
3334492 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.76 68.0 6.45e-01 97.1% 83.7%
3664743 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.76 68.0 6.05e-01 97.1% 83.2%
3448800 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.74 68.0 5.74e-01 100.0% 74.5%
3657923 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.74 67.0 6.00e-01 100.0% 83.2%
3428327 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.70 63.0 4.69e-01 100.0% 47.6%
4944466 301.13.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain 0.69 51.0 4.25e-01 79.7% 74.4%
4134161 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.66 46.0 3.74e-01 73.9% 71.9%
2162577 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.64 47.0 3.82e-01 78.3% 67.9%
4480622 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.64 44.0 3.64e-01 72.5% 79.1%
3424354 226.1.1.20 ↗ a+b two layers › POZ domain › POZ domain › POZ domain › PF30468, PF30469 0.57 42.0 3.10e-01 78.3% 92.1%
3600916 2004.1.1.144 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DEAD_2 0.57 44.0 2.93e-01 87.0% 20.4%
4316396 327.11.2.73 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Eukaryotic type KH-domain (KH-domain type I) › HD 0.55 41.0 2.95e-01 84.1% 90.4%
5036902 2002.1.1.60 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › AP_endonuc_2 0.54 40.0 2.54e-01 79.7% 31.7%
3391689 5054.1.1.1 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Lig_chan 0.54 39.0 2.94e-01 78.3% 51.7%
3170748 141.1.1.1 ↗ alpha bundles › Terpenoid synthases › Terpenoid synthases › Terpenoid synthases › polyprenyl_synt 0.54 39.0 2.47e-01 76.8% 39.9%
4943574 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.54 42.0 3.42e-01 88.4% 58.6%
3969156 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.53 45.0 3.63e-01 98.6% 96.6%
None — 0.53 45.0 2.64e-01 98.6% 52.1%
3936954 7579.1.1.14 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Lipase_3 0.52 42.0 2.90e-01 91.3% 28.6%
3983196 2498.1.1.57 ↗ mixed a+b and a/b › Zincin-like › "Metalloproteases (""zincins"") catalytic domain" › "Metalloproteases (""zincins"") catalytic domain" › LPD1 0.52 45.0 3.17e-01 98.6% 60.4%
5034583 1001.1.1.0 ↗ a+b two layers › Formate dehydrogenase/DMSO reductase, domain 1 › Formate dehydrogenase/DMSO reductase, domain 1 › Formate dehydrogenase/DMSO reductase, domain 1 0.52 33.0 3.78e-01 84.1% 90.0%
4022052 108.1.1.11 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand › Cullin_binding 0.52 43.0 3.67e-01 100.0% 90.4%
4113 141.1.1.1 ↗ alpha bundles › Terpenoid synthases › Terpenoid synthases › Terpenoid synthases › polyprenyl_synt 0.51 41.0 2.86e-01 95.7% 77.1%
4437052 167.1.1.1 ↗ alpha arrays › Ribosomal protein S7 › Ribosomal protein S7 › Ribosomal protein S7 › Ribosomal_S7 0.51 44.0 3.46e-01 98.6% 78.0%
D3 high residues 222-292
PDB
Domain cluster: rep: LC768487.1__BEH88345.1__X__00057__D137-205
CATH (18)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1gccA00 3.30.730.10 Alpha Beta › 2-Layer Sandwich › GCC-box Binding Domain › AP2/ERF domain 0.88 60.0 6.34e-01 70.4% 88.9%
7wq5A01 3.30.730.10 Alpha Beta › 2-Layer Sandwich › GCC-box Binding Domain › AP2/ERF domain 0.86 61.0 6.69e-01 73.2% 100.0%
1mgpA02 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.67 46.0 3.90e-01 71.8% 67.8%
3nyiA02 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.67 46.0 3.74e-01 71.8% 68.6%
2vgnA02 3.30.420.60 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › eRF1 domain 2 0.63 43.0 3.59e-01 71.8% 59.8%
2ivnA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.61 41.0 3.28e-01 70.4% 92.4%
4yg6B00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.61 46.0 3.58e-01 83.1% 68.7%
1f6kC00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.59 51.0 3.43e-01 98.6% 83.5%
2zihC00 1.10.3630.10 Mainly Alpha › Orthogonal Bundle › yeast vps74-n-term truncation variant fold › yeast vps74-n-term truncation variant domain like 0.57 46.0 3.12e-01 90.1% 100.0%
1uajA02 1.10.1270.20 Mainly Alpha › Orthogonal Bundle › Trp Operon Repressor; Chain A › tRNA(m1g37)methyltransferase, domain 2 0.55 40.0 4.00e-01 100.0% 75.3%
3jr1A02 3.90.1200.10 Alpha Beta › Alpha-Beta Complex › Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 › Aminoglycoside phosphotransferase (APH), C-terminal lobe 0.55 47.0 3.54e-01 100.0% 79.2%
2zbkA01 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 0.55 41.0 3.52e-01 81.7% 85.1%
4n4pD00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.55 47.0 3.19e-01 98.6% 83.3%
5hn3A00 3.40.718.10 Alpha Beta › 3-Layer(aba) Sandwich › Isopropylmalate Dehydrogenase › Isopropylmalate Dehydrogenase 0.55 40.0 2.60e-01 78.9% 84.6%
2xseA00 1.20.120.1440 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › JBP1, DNA-binding domain 0.53 45.0 3.56e-01 98.6% 93.1%
1pzxA03 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.51 44.0 3.74e-01 98.6% 91.0%
4mtlA00 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.51 41.0 3.02e-01 93.0% 33.7%
6dgiA02 3.30.470.20 Alpha Beta › 2-Layer Sandwich › D-amino Acid Aminotransferase; Chain A, domain 1 › ATP-grasp fold, B domain 0.50 39.0 3.12e-01 84.5% 65.3%
ECOD (30)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3467141 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.83 76.0 6.50e-01 100.0% 76.4%
3293480 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.79 62.0 6.53e-01 88.7% 90.8%
3299337 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.78 67.0 5.98e-01 93.0% 85.7%
3370971 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.77 66.0 6.07e-01 93.0% 92.2%
3827127 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.77 66.0 5.88e-01 91.5% 80.0%
3331331 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.76 67.0 5.86e-01 93.0% 77.0%
3651077 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.76 62.0 6.27e-01 87.3% 100.0%
3334492 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.76 66.0 6.33e-01 93.0% 83.7%
3657923 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.75 66.0 5.94e-01 94.4% 84.2%
3448800 252.2.1.1 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › AP2 0.75 66.0 5.63e-01 94.4% 74.5%
3664743 252.2.1.0 ↗ a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like 0.74 64.0 5.73e-01 93.0% 83.2%
1937542 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.67 46.0 3.86e-01 71.8% 68.3%
4944466 301.13.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain 0.67 47.0 3.93e-01 73.2% 73.6%
3281041 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.65 45.0 3.70e-01 71.8% 69.2%
4944129 301.13.1.0 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain 0.63 44.0 3.67e-01 73.2% 72.3%
3962875 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.63 44.0 3.68e-01 74.6% 69.2%
4626818 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.61 41.0 3.64e-01 70.4% 60.0%
3974750 4040.1.1.1 ↗ alpha bundles › Fic-like › Fic-like › Fic-like › Fic 0.59 44.0 2.92e-01 78.9% 65.9%
4349801 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.59 41.0 3.46e-01 73.2% 71.9%
4538897 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.58 40.0 3.46e-01 74.6% 71.8%
3169173 3241.1.1.1 ↗ alpha arrays › Golgi phosphoprotein 3 › Golgi phosphoprotein 3 › Golgi phosphoprotein 3 › GPP34 0.57 47.0 3.22e-01 94.4% 100.0%
5082053 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.56 46.0 3.20e-01 91.5% 32.7%
3700687 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.55 39.0 2.67e-01 74.6% 42.4%
3244475 4156.1.1.3 ↗ alpha arrays › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › Sec63 N-terminal subdomain-like › DSHCT 0.54 41.0 3.19e-01 83.1% 40.0%
3424354 226.1.1.20 ↗ a+b two layers › POZ domain › POZ domain › POZ domain › PF30468, PF30469 0.51 40.0 2.96e-01 84.5% 79.5%
1933261 301.13.1.1 ↗ a+b three layers › Bacillus chorismate mutase-like › DAK1/DegV C-terminal domain › DAK1/DegV C-terminal domain › DegV 0.51 44.0 3.75e-01 98.6% 91.7%
5059362 4271.1.1.3 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like › DNA_primase_lrg_N 0.51 43.0 3.12e-01 100.0% 96.1%
3484278 873.1.1.0 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain 0.51 36.0 2.65e-01 74.6% 93.3%
5082216 4271.1.1.3 ↗ alpha complex topology › PriB N-terminal domain-like › PriB N-terminal domain-like › PriB N-terminal domain-like › DNA_primase_lrg_N 0.51 42.0 3.18e-01 98.6% 99.0%
5046452 632.1.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.51 39.0 3.21e-01 83.1% 77.7%