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MW749006.1__QXN70534.1__AGENTSMITH_130__00128

Bact-Vir

MW749006.1__QXN70534.1__AGENTSMITH_130__00128

Identity

Accession:
MW749006 ↗
Kingdom:
phage

Quality

71.9 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Bacillus_phage_vB_BspM_AgentSmith

TaxID: 2836110

Cluster

View cluster (9 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 4-77_275-303
PDB
Domain cluster: rep: MW879341.1__QXO11119.1__pEaSNUABM54_00293__00293__D1-70_267-286
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
5hr9A02 3.30.210.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 3 › DNA polymerase, thumb domain 0.66 35.0 4.19e-01 90.3% 76.8%
2bcqA04 3.30.210.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 3 › DNA polymerase, thumb domain 0.55 35.0 4.20e-01 88.3% 98.5%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4951202 316.1.1.23 ↗ a+b three layers › Nucleotidyltransferase-like › Nucleotidyltransferase › Nucleotidyltransferase › DNA_pol_B_thumb 0.57 36.0 3.11e-01 87.4% 41.9%
D2 medium residues 78-139_231-274
PDB
Domain cluster: representative
CATH (27)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2qffA00 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.66 43.0 5.08e-01 85.8% 95.9%
1oahA02 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.62 55.0 4.99e-01 96.2% 73.9%
4xvxA03 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 55.0 4.94e-01 100.0% 87.1%
6zhiB02 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.60 44.0 4.93e-01 88.7% 98.8%
1sj8A02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.60 54.0 5.20e-01 100.0% 93.4%
6p73A02 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.59 51.0 4.58e-01 92.5% 67.8%
3fhnA05 1.10.10.2270 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Dsl1p vesicle tethering complex, Tip20p subunit, domain E 0.59 30.0 3.64e-01 90.6% 74.6%
4e40A00 1.20.1260.80 Mainly Alpha › Up-down Bundle › Ferritin › 0.59 49.0 3.70e-01 88.7% 80.4%
3o6xA02 1.20.120.1560 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.59 51.0 4.60e-01 95.3% 87.2%
1hs7A00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.59 32.0 3.41e-01 74.5% 58.8%
1qdbA02 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.58 50.0 4.50e-01 93.4% 68.5%
3nvoB02 1.20.58.340 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Magnesium transport protein CorA, transmembrane region 0.58 48.0 4.70e-01 87.7% 87.9%
3m9vA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.57 51.0 4.54e-01 100.0% 91.7%
2c0uA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.57 52.0 4.43e-01 100.0% 85.2%
2vxxA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.57 46.0 3.94e-01 87.7% 83.7%
4etrB00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.54 44.0 4.24e-01 87.7% 95.9%
2qywA00 1.20.58.400 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › t-snare proteins 0.54 44.0 4.68e-01 87.7% 96.8%
3hwcA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.53 48.0 3.85e-01 100.0% 78.6%
8d7hD01 1.20.1250.10 Mainly Alpha › Up-down Bundle › Growth Hormone; Chain: A; › 0.53 48.0 4.10e-01 100.0% 62.4%
3e6sA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.53 46.0 4.05e-01 100.0% 64.2%
7e5aB02 1.20.1000.10 Mainly Alpha › Up-down Bundle › Signaling Protein - Interferon-induced Guanylate-binding Protein 1; Chain A, domain 1 › Guanylate-binding protein, C-terminal domain 0.52 33.0 2.83e-01 100.0% 40.2%
4h63H01 1.20.58.1710 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.52 34.0 4.06e-01 100.0% 97.2%
2yfaA02 1.20.1440.210 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.52 47.0 4.57e-01 100.0% 90.5%
2hfiA00 1.20.120.440 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › YppE-like 0.52 39.0 3.77e-01 88.7% 69.1%
5dvwA00 1.20.120.1160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.51 40.0 3.73e-01 84.0% 65.9%
2dfkC01 1.20.900.10 Mainly Alpha › Up-down Bundle › Dbl Homology Domain; Chain A › Dbl homology (DH) domain 0.51 46.0 3.67e-01 100.0% 66.0%
6z74C02 1.20.120.530 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › GntR ligand-binding domain-like 0.51 42.0 3.68e-01 96.2% 59.1%
ECOD (27)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4683070 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.64 37.0 3.36e-01 100.0% 44.3%
3246244 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.62 58.0 4.37e-01 100.0% 52.9%
3633174 604.1.1.55 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › RasGAP_C 0.61 46.0 4.82e-01 87.7% 84.0%
3810521 633.4.1.1 ↗ alpha bundles › Bromodomain-like › Plant invertase/pectin methylesterase inhibitor › Plant invertase/pectin methylesterase inhibitor › PMEI 0.61 55.0 5.01e-01 99.1% 92.9%
3521820 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.60 34.0 2.58e-01 88.7% 24.7%
3989535 632.6.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Plasmid maintenance system epsilon/zeta, antidote epsilon subunit › Plasmid maintenance system epsilon/zeta, antidote epsilon subunit 0.59 45.0 4.78e-01 88.7% 89.5%
3870615 633.23.1.34 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › CD20 0.59 53.0 5.03e-01 99.1% 96.8%
3873872 633.21.1.23 ↗ alpha bundles › Bromodomain-like › Uncharacterized protein PA2107 › Uncharacterized protein PA2107 › CD20 0.59 53.0 4.54e-01 100.0% 83.5%
5074552 192.15.1.0 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.58 35.0 3.43e-01 100.0% 55.7%
4026713 3684.1.1.0 ↗ alpha complex topology › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like › PSPTO4464 C-terminal domain-like 0.56 47.0 3.92e-01 88.7% 73.1%
3462885 192.15.1.0 ↗ alpha bundles › Long alpha-hairpin › Endosomal sorting complex assembly domains › Endosomal sorting complex assembly domains 0.55 49.0 4.13e-01 100.0% 68.1%
3227635 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.55 49.0 4.31e-01 99.1% 95.6%
3793999 604.1.1.118 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › GOSR1_N 0.55 47.0 4.20e-01 90.6% 81.4%
5064406 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.55 49.0 4.77e-01 99.1% 92.5%
3409848 3285.1.1.1 ↗ alpha duplicates or obligate multimers › Alix V domain › Alix V domain › Alix V domain › ALIX_LYPXL_bnd 0.55 45.0 3.17e-01 88.7% 72.7%
3362472 605.1.1.132 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › DUF641 0.55 44.0 4.40e-01 88.7% 83.6%
4535751 1189.1.1.0 ↗ alpha bundles › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor › VSG (variant surface glycoprotein) N-terminal domain and haptoglobin-hemoglobin receptor 0.55 46.0 3.15e-01 91.5% 86.5%
3491130 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.54 45.0 4.13e-01 88.7% 92.6%
3939240 174.1.1.0 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain 0.54 47.0 4.27e-01 96.2% 93.6%
3465357 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.53 44.0 4.34e-01 87.7% 84.3%
3743554 603.1.1.99 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › PF27021 0.53 50.0 4.49e-01 100.0% 87.1%
5014639 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 0.53 43.0 4.46e-01 86.8% 94.0%
3627804 133.1.1.1 ↗ alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) › RhoGEF 0.52 46.0 3.64e-01 100.0% 66.7%
4098159 601.23.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › DNA repair protein MutS, domain III › DNA repair protein MutS, domain III 0.51 41.0 3.03e-01 100.0% 32.9%
3782610 606.1.1.1 ↗ alpha complex topology › Nop N-terminal domain › Nop N-terminal domain › Nop N-terminal domain › Nop 0.51 42.0 3.45e-01 88.7% 83.7%
3585389 7087.1.1.0 ↗ alpha bundles › Emopamil binding protein (EBP) transmembrane domain › Emopamil binding protein (EBP) transmembrane domain › Emopamil binding protein (EBP) transmembrane domain 0.50 41.0 3.84e-01 87.7% 96.2%
3512539 133.1.1.1 ↗ alpha bundles › DH domain-like › DBL homology domain (DH-domain) › DBL homology domain (DH-domain) › RhoGEF 0.50 45.0 3.58e-01 100.0% 82.3%
D3 medium residues 140-230
PDB
Domain cluster: rep: pre3_saliva_scaffold_6_prodigal-single.1__X__X__00066__D127-235
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1k8iB01 3.10.320.10 Alpha Beta › Roll › Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 › Class II Histocompatibility Antigen, M Beta Chain; Chain B, domain 1 0.51 42.0 4.20e-01 100.0% 91.2%
3bemB00 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.51 43.0 3.30e-01 93.4% 68.9%
1icrA00 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.50 41.0 3.22e-01 93.4% 74.5%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4035686 4959.1.1.1 ↗ a+b complex topology › first helical domain in RNA-polymerase beta-prime subunit › first helical domain in RNA-polymerase beta-prime subunit › first helical domain in RNA-polymerase beta-prime subunit › RNA_pol_Rpb1_3 0.61 34.0 2.94e-01 92.3% 34.3%
3915239 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.59 31.0 2.41e-01 100.0% 23.6%
3220970 389.1.2.1 ↗ few secondary structure elements › EGF-like › EGF-related › Complement control module/SCR domain › Sushi 0.57 28.0 3.28e-01 90.1% 64.7%
3991841 389.1.2.1 ↗ few secondary structure elements › EGF-like › EGF-related › Complement control module/SCR domain › Sushi 0.56 28.0 3.29e-01 91.2% 67.7%
3439912 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.54 30.0 2.98e-01 100.0% 49.0%
3812213 2484.1.1.9 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › rve 0.53 30.0 2.46e-01 97.8% 29.7%
4425065 3281.1.1.2 ↗ alpha complex topology › Sodium/proton antiporter subunits-like › Sodium/proton antiporter subunits-like › NADH-quinone oxidoreductase subunit L (NuoL)-related › Proton_antipo_M,Proton_antipo_N 0.51 42.0 2.59e-01 95.6% 33.8%
5056444 2002.1.1.29 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › DHDPS 0.51 39.0 2.67e-01 83.5% 24.6%
3655782 101.1.2.598 ↗ alpha arrays › HTH › HTH › winged helix domain › RNA_pol_Rpc82, POLR3C_WHD 0.51 38.0 2.68e-01 81.3% 81.6%