←Back to structures

MK433275.1__QAY17611.1__SEA_EMSQUAREDA_8__00008

Bact-Vir

MK433275.1__QAY17611.1__SEA_EMSQUAREDA_8__00008

Identity

Accession:
MK433275 ↗
Kingdom:
phage

Quality

75.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Gordonia_phage_EMsquaredA

TaxID: 2510503

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 6-47
PDB
Domain cluster: representative
CATH (11)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1s7iA00 3.30.70.1060 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Dimeric alpha+beta barrel 0.66 40.0 2.90e-01 88.1% 20.2%
2hc8A00 2.70.150.10 Mainly Beta › Distorted Sandwich › Calcium-transporting ATPase, cytoplasmic transduction domain A › Calcium-transporting ATPase, cytoplasmic transduction domain A 0.64 56.0 4.11e-01 100.0% 39.8%
7nz1G01 2.40.40.20 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › 0.60 43.0 3.40e-01 81.0% 66.7%
3kmhA00 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.58 45.0 3.01e-01 100.0% 22.9%
2q2gB02 2.60.260.20 Mainly Beta › Sandwich › HSP40/DNAj peptide-binding domain › Urease metallochaperone UreE, N-terminal domain 0.56 40.0 3.37e-01 78.6% 65.8%
4iv9A03 1.10.405.40 Mainly Alpha › Orthogonal Bundle › Guanine Nucleotide Dissociation Inhibitor; domain 1 › 0.53 39.0 2.87e-01 92.9% 95.3%
5f29B00 3.30.70.1450 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Regulator of K+ conductance, C-terminal domain 0.53 38.0 3.44e-01 85.7% 70.4%
2jxtA01 3.10.20.10 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.53 38.0 3.26e-01 81.0% 69.7%
6whcA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 36.0 2.33e-01 73.8% 74.9%
1yfbA00 2.10.260.10 Mainly Beta › Ribbon › Pemi-like Protein 1; Chain: D › 0.51 32.0 3.06e-01 71.4% 38.5%
1wlfA01 2.40.40.20 Mainly Beta › Beta Barrel › Barwin-like endoglucanases › 0.51 37.0 3.17e-01 88.1% 76.2%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4939413 4076.3.1.0 ↗ a+b two layers › L9 N-domain-like › GINS/PriA/YqbF domain › GINS/PriA/YqbF domain 0.64 52.0 5.07e-01 100.0% 94.0%
5023856 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.61 49.0 4.03e-01 95.2% 85.9%
4299573 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.59 42.0 3.25e-01 78.6% 59.0%
5075881 207.2.1.13 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like › NosD 0.58 41.0 2.29e-01 78.6% 15.1%
3967671 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.57 42.0 3.26e-01 81.0% 60.0%
3604712 1189.1.1.1 ↗ 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 › Trypan_glycop 0.56 40.0 2.39e-01 81.0% 82.1%
4816887 5054.1.1.2 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › Ion_trans 0.56 35.0 2.54e-01 90.5% 17.6%
5079518 2.1.1.83 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › SfsA_N 0.55 36.0 3.47e-01 78.6% 58.0%
4639978 1.1.3.2 ↗ beta barrels › cradle loop barrel › RIFT-related › AbrB › MazE_antitoxin 0.54 34.0 3.17e-01 83.3% 41.8%
3391397 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.54 42.0 3.41e-01 88.1% 74.4%
4972671 207.2.1.0 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Pectin lyase-like › Pectin lyase-like 0.54 37.0 2.28e-01 76.2% 24.1%
4856387 5001.1.1.1 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7tm_1 0.53 36.0 2.32e-01 90.5% 13.6%
5003070 304.24.1.5 ↗ a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like › Trm5_N 0.52 40.0 3.68e-01 88.1% 98.3%
3310260 109.4.1.1269 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, E_motif 0.51 37.0 2.15e-01 85.7% 8.6%
3335423 109.4.1.1993 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, E_motif, TPR_24 0.50 34.0 1.90e-01 71.4% 4.7%
D2 high residues 69-104
PDB
Domain cluster: representative
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4aidA02 1.10.10.400 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Polyribonucleotide nucleotidyltransferase, RNA-binding domain 0.75 51.0 3.90e-01 72.2% 46.3%
1s2xA00 1.20.190.30 Mainly Alpha › Up-down Bundle › Delta-Endotoxin; domain 1 › CAG pathogenicity island protein, CagZ 0.73 50.0 3.20e-01 72.2% 16.1%
1f7cA00 1.10.555.10 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase; Chain A › Rho GTPase activation protein 0.69 48.0 3.03e-01 72.2% 20.3%
1jr8A00 1.20.120.310 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › ERV/ALR sulfhydryl oxidase domain 0.68 55.0 4.03e-01 94.4% 62.9%
2y4tA02 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.68 46.0 4.11e-01 72.2% 63.5%
3no6A00 1.20.910.10 Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like 0.67 50.0 3.09e-01 83.3% 77.9%
2o4cA03 3.30.1370.170 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › Erythronate-4-phosphate dehydrogenase, dimerisation domain 0.66 46.0 3.48e-01 72.2% 31.8%
3a6pA00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.65 53.0 2.80e-01 100.0% 8.2%
2ee4A01 1.10.555.10 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase; Chain A › Rho GTPase activation protein 0.65 45.0 2.84e-01 72.2% 17.2%
2oh3A01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.64 55.0 3.69e-01 100.0% 47.2%
3h7iA02 1.10.150.20 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › 5' to 3' exonuclease, C-terminal subdomain 0.63 43.0 3.48e-01 75.0% 90.9%
3t6gB00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.63 50.0 3.54e-01 100.0% 60.4%
3m1cB01 3.30.390.170 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › 0.62 46.0 3.21e-01 80.6% 29.4%
3eoqB02 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.61 49.0 3.11e-01 88.9% 54.6%
4hkaA02 1.10.287.3810 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.61 44.0 3.92e-01 97.2% 54.9%
5ux1D00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.56 46.0 2.89e-01 94.4% 36.5%
2jpnA00 1.20.1280.210 Mainly Alpha › Up-down Bundle › Monooxygenase › Uncharacterised protein UvsW.1 0.55 44.0 3.58e-01 100.0% 70.9%
3s64A00 1.10.225.10 Mainly Alpha › Orthogonal Bundle › NK-Lysin › Saposin-like 0.53 40.0 3.22e-01 94.4% 39.5%
3ihjA02 1.10.287.1970 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.52 44.0 4.41e-01 94.4% 92.1%
ECOD (13)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3966774 101.11.1.0 ↗ alpha arrays › HTH › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 › Polynucleotide phosphorylase/guanosine pentaphosphate synthase (PNPase/GPSI), domain 3 0.76 52.0 3.99e-01 72.2% 36.3%
4393704 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.73 64.0 3.52e-01 100.0% 23.2%
3302917 2004.1.1.505 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_11, AAA_30 0.68 46.0 2.67e-01 72.2% 10.6%
4954644 192.7.1.0 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm 0.67 46.0 3.15e-01 72.2% 29.2%
3716015 4970.1.1.0 ↗ alpha bundles › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I › fingers domain in bacteriophage RB69-like DNA polymerase I 0.67 45.0 3.84e-01 72.2% 58.3%
3355429 150.1.1.0 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › Ferritin/Heme oxygenase › Ferritin 0.66 47.0 3.80e-01 75.0% 53.8%
3496789 5054.1.1.17 ↗ alpha complex topology › Voltage-gated ion channels › Voltage-gated ion channels › Voltage-gated ion channels › TRAM_LAG1_CLN8 0.66 49.0 3.00e-01 86.1% 13.7%
3987389 2004.1.1.5 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.65 54.0 3.02e-01 97.2% 13.3%
3741785 4006.1.1.1 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.65 44.0 3.22e-01 72.2% 35.0%
4429835 4006.1.1.1 ↗ alpha bundles › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › Release factor (Pfam 00472) N-terminal alpha helical domain › PCRF 0.59 43.0 3.24e-01 83.3% 99.0%
5073477 4969.1.1.1 ↗ alpha bundles › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I › DNA_pol_B 0.58 49.0 3.26e-01 97.2% 64.0%
3170733 109.4.1.3117 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PF30095 0.57 45.0 2.87e-01 100.0% 26.1%
5077689 4163.1.1.0 ↗ alpha bundles › GINS helical bundle-like › GINS helical bundle-like › PSF1 N-terminal domain-like 0.54 48.0 3.29e-01 100.0% 62.5%