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LC680885.1__BDE75600.1__X__00062

Bact-Vir

LC680885.1__BDE75600.1__X__00062

Identity

Accession:
LC680885 ↗
Kingdom:
phage

Quality

78.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Staphylococcus_phage_S6

TaxID: 2913378

Cluster

View cluster (2 members)

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 medium residues 1-51_179-202
PDB
Domain cluster: representative
CATH (27)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4i9fA03 3.30.300.290 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › 0.64 43.0 4.31e-01 76.0% 67.5%
3pbkA02 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.62 51.0 4.56e-01 92.0% 73.1%
4ekfA00 3.40.395.10 Alpha Beta › 3-Layer(aba) Sandwich › Adenoviral Proteinase; Chain › Adenoviral Proteinase; Chain A 0.61 53.0 3.96e-01 97.3% 65.6%
2bh1X00 3.30.300.160 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › Type II secretion system, protein E, N-terminal domain 0.60 41.0 4.25e-01 84.0% 76.5%
1vw5A00 3.30.70.1420 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Structure from the mobile metagenome of cole harbour salt marsh: integron cassette protein hfx_cass1 0.59 50.0 4.07e-01 97.3% 59.6%
4alzA03 3.30.70.1770 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 37.0 3.98e-01 74.7% 76.6%
2l72A00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.58 45.0 3.94e-01 88.0% 55.1%
1vkcA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.57 39.0 3.26e-01 73.3% 85.6%
4alzA01 3.30.1340.30 Alpha Beta › 2-Layer Sandwich › Histidine-containing Protein; Chain: A; › 0.57 35.0 3.72e-01 76.0% 72.6%
2cxcA02 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.56 39.0 4.06e-01 73.3% 81.2%
3m6nA01 3.90.226.10 Alpha Beta › Alpha-Beta Complex › 2-enoyl-CoA Hydratase; Chain A, domain 1 › 2-enoyl-CoA Hydratase; Chain A, domain 1 0.55 46.0 3.41e-01 96.0% 97.6%
1l1lA01 3.20.70.20 Alpha Beta › Alpha-Beta Barrel › Anaerobic Ribonucleotide-triphosphate Reductase Large Chain › 0.54 41.0 2.56e-01 85.3% 81.6%
8a9nA01 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.54 38.0 3.24e-01 74.7% 86.3%
6vhvA01 3.30.300.30 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › ANL, C-terminal domain 0.53 43.0 4.07e-01 92.0% 76.3%
2ql8A00 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.53 41.0 3.37e-01 85.3% 49.3%
1josA00 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.52 38.0 3.55e-01 80.0% 72.0%
3bamA00 3.40.91.20 Alpha Beta › 3-Layer(aba) Sandwich › Restriction Endonuclease › 0.52 35.0 2.62e-01 72.0% 89.3%
2lxxA00 3.40.20.10 Alpha Beta › 3-Layer(aba) Sandwich › Severin › Severin 0.52 43.0 3.55e-01 98.7% 59.9%
2fiaB00 3.40.630.30 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT) 0.51 41.0 3.27e-01 89.3% 80.5%
4c1sA00 1.50.10.20 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.51 44.0 2.88e-01 100.0% 52.5%
2jvfA00 3.30.1710.10 Alpha Beta › 2-Layer Sandwich › top7, de novo designed protein › top7, de novo designed protein 0.51 36.0 3.38e-01 74.7% 92.6%
2pt7G01 3.30.300.20 Alpha Beta › 2-Layer Sandwich › GMP Synthetase; Chain A, domain 3 › K homology (KH) domain 0.51 36.0 3.63e-01 76.0% 79.5%
1xm8A00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.51 44.0 3.08e-01 97.3% 36.6%
3k6jA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.51 42.0 3.13e-01 97.3% 73.8%
1rm6A01 3.30.365.10 Alpha Beta › 2-Layer Sandwich › Aldehyde Oxidoreductase; domain 4 › Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain 0.51 38.0 3.33e-01 82.7% 76.5%
8d3mI01 3.90.320.10 Alpha Beta › Alpha-Beta Complex › Lambda Exonuclease; Chain A › 0.51 39.0 2.92e-01 85.3% 55.1%
1ffvB05 3.30.365.10 Alpha Beta › 2-Layer Sandwich › Aldehyde Oxidoreductase; domain 4 › Aldehyde oxidase/xanthine dehydrogenase, molybdopterin binding domain 0.50 38.0 3.53e-01 81.3% 81.4%
ECOD (31)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3437716 219.1.1.16 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › Peptidase_C48 0.67 53.0 4.52e-01 86.7% 65.0%
3970701 560.1.1.0 ↗ few secondary structure elements › H-NS histone-like proteins, C-terminal domain › H-NS histone-like proteins, C-terminal domain › H-NS histone-like proteins, C-terminal domain 0.64 28.0 3.72e-01 94.7% 75.0%
3578869 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.60 41.0 2.84e-01 72.0% 84.4%
4028488 224.1.1.0 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like 0.59 51.0 4.24e-01 100.0% 52.9%
1565126 3261.1.1.7 ↗ a+b two layers › amino-terminal domain of OmpATb › amino-terminal domain of OmpATb › amino-terminal domain of OmpATb › CdsD_PD1 0.59 37.0 3.88e-01 74.7% 70.8%
4943143 224.1.1.0 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like 0.59 47.0 4.45e-01 92.0% 73.3%
4442243 327.1.1.1 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Alpha-lytic protease prodomain › Alpha-lytic protease prodomain › Pro_Al_protease 0.58 36.0 3.70e-01 76.0% 65.7%
3486794 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 50.0 3.97e-01 100.0% 87.5%
3641547 327.10.1.9 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Ribosome-binding factor A (RbfA)-related › Ribosome-binding factor A (RbfA)-related › DnaA_N-like_STI 0.57 40.0 3.77e-01 76.0% 61.1%
3940245 213.1.1.31 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_10 0.56 39.0 3.26e-01 73.3% 83.1%
4186952 327.5.1.2 ↗ a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins › AMP-binding_C 0.55 45.0 4.03e-01 90.7% 73.6%
4991181 327.11.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) 0.55 37.0 3.87e-01 74.7% 80.0%
3580539 327.2.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › BolA-like › BolA-like 0.55 38.0 3.52e-01 73.3% 84.7%
3960824 327.11.1.7 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) › KH_NusA_2nd 0.54 36.0 3.72e-01 80.0% 74.3%
3979017 327.11.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) 0.54 37.0 3.75e-01 78.7% 72.0%
3617340 327.10.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Ribosome-binding factor A (RbfA)-related › Ribosome-binding factor A (RbfA)-related 0.54 39.0 3.52e-01 78.7% 61.8%
4976070 327.7.1.17 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Cation efflux protein cytoplasmic domain-like › Cation efflux protein cytoplasmic domain-like › EFG_C 0.54 33.0 3.58e-01 76.0% 76.7%
4979820 224.1.1.0 ↗ a+b three layers › Gelsolin-like › Gelsolin-like › Gelsolin-like 0.53 39.0 3.87e-01 78.7% 77.5%
4134060 327.10.1.2 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Ribosome-binding factor A (RbfA)-related › Ribosome-binding factor A (RbfA)-related › RBFA 0.53 37.0 3.49e-01 74.7% 71.6%
3939245 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 0.52 39.0 2.57e-01 81.3% 86.2%
3940554 2007.2.3.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II 0.52 44.0 2.98e-01 96.0% 64.1%
5055415 2004.1.1.42 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE 0.52 43.0 2.68e-01 96.0% 45.6%
3588613 327.11.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) 0.51 36.0 3.66e-01 73.3% 78.1%
4979047 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.51 41.0 3.26e-01 89.3% 55.2%
4983425 2004.1.1.42 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › T2SSE 0.51 41.0 2.62e-01 96.0% 43.2%
5030033 327.11.1.0 ↗ a+b two layers › Alpha-lytic protease prodomain-like › KH-domains › Prokaryotic type KH domain (KH-domain type II) 0.51 34.0 3.63e-01 70.7% 83.1%
4416595 327.10.1.2 ↗ a+b two layers › Alpha-lytic protease prodomain-like › Ribosome-binding factor A (RbfA)-related › Ribosome-binding factor A (RbfA)-related › RBFA 0.51 38.0 3.36e-01 81.3% 57.4%
4944397 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.50 27.0 3.11e-01 90.7% 74.0%
3260134 622.4.1.61 ↗ alpha bundles › YvfG-like › Mite allergen Der p 5-related › Mite allergen Der p 5-related › Mit_KHE1 0.50 37.0 3.05e-01 80.0% 94.5%
4976411 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.50 41.0 2.56e-01 96.0% 45.2%
3580028 2007.2.3.1 ↗ a/b three-layered sandwiches › Flavodoxin-like › Flavoproteins/Phosphotyrosine protein phosphatases-like › (Phosphotyrosine protein) phosphatases II › Y_phosphatase 0.50 41.0 3.09e-01 92.0% 91.6%
D2 medium residues 52-178
PDB
Domain cluster: representative
CATH (14)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3n8bA00 3.10.450.700 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.70 35.0 4.58e-01 79.5% 84.0%
3wa5B00 2.60.120.1690 Mainly Beta › Sandwich › Jelly Rolls › 0.63 34.0 3.50e-01 85.8% 53.2%
5ds1A00 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.61 35.0 4.09e-01 85.8% 78.3%
6yfiB01 3.30.380.10 Alpha Beta › 2-Layer Sandwich › MS2 Viral Coat Protein › MS2 Viral Coat Protein 0.59 42.0 4.16e-01 89.0% 69.6%
7vd7A01 3.10.450.530 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › Ribonuclease toxin, BrnT, of type II toxin-antitoxin system 0.58 28.0 3.24e-01 73.2% 59.8%
2vf9A00 3.30.380.10 Alpha Beta › 2-Layer Sandwich › MS2 Viral Coat Protein › MS2 Viral Coat Protein 0.58 40.0 4.01e-01 86.6% 67.9%
4h5bA00 3.30.1460.70 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.54 47.0 4.45e-01 95.3% 96.1%
2giaB00 2.30.31.40 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › 0.53 45.0 4.27e-01 96.1% 78.8%
1qj8A00 2.40.160.20 Mainly Beta › Beta Barrel › Porin › 0.51 44.0 4.18e-01 92.9% 93.2%
3ia8A00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.51 44.0 4.11e-01 95.3% 97.5%
1y0gA00 2.40.128.110 Mainly Beta › Beta Barrel › Lipocalin › Lipid/polyisoprenoid-binding, YceI-like 0.51 43.0 3.97e-01 93.7% 96.4%
1p4tA00 2.40.160.20 Mainly Beta › Beta Barrel › Porin › 0.50 43.0 4.09e-01 94.5% 93.5%
3ir3A00 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.50 35.0 3.57e-01 71.7% 100.0%
2gvhC01 3.10.129.10 Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase 0.50 35.0 3.44e-01 70.9% 91.9%
ECOD (18)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4030444 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.65 48.0 5.10e-01 91.3% 88.2%
169039 265.1.1.1 ↗ a+b two layers › RNA bacteriophage capsid protein › RNA bacteriophage capsid protein › RNA bacteriophage capsid protein › Levi_coat 0.58 40.0 4.01e-01 86.6% 67.9%
3718060 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.58 44.0 4.61e-01 96.1% 87.0%
3808882 4051.1.1.1 ↗ a+b two layers › a+b domain in Capz › a+b domain in Capz › a+b domain in Capz › F_actin_cap_B 0.58 49.0 4.42e-01 92.1% 68.6%
4966376 2484.1.1.59 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › NurA 0.58 42.0 3.14e-01 75.6% 67.0%
3326287 4051.1.1.1 ↗ a+b two layers › a+b domain in Capz › a+b domain in Capz › a+b domain in Capz › F_actin_cap_B 0.57 48.0 4.94e-01 92.1% 97.5%
3344144 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.56 33.0 3.91e-01 76.4% 85.7%
3787225 4051.1.1.1 ↗ a+b two layers › a+b domain in Capz › a+b domain in Capz › a+b domain in Capz › F_actin_cap_B 0.56 47.0 4.08e-01 91.3% 77.9%
3591111 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.56 42.0 2.83e-01 78.7% 32.7%
5043858 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.55 45.0 4.45e-01 92.1% 96.4%
3608101 330.1.1.0 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.54 37.0 4.14e-01 85.0% 92.6%
3265120 1.1.5.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.54 39.0 3.52e-01 75.6% 96.0%
3449012 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.54 41.0 4.36e-01 96.1% 91.8%
3909452 5.1.4.223 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_RIC1_2nd 0.52 47.0 2.86e-01 100.0% 47.8%
3783604 222.1.1.4 ↗ a+b two layers › Thioesterase/thiol ester dehydrase-isomerase-like › Thioesterase/thiol ester dehydrase-isomerase › Thioesterase/thiol ester dehydrase-isomerase › 4HBT 0.52 38.0 3.21e-01 74.8% 70.7%
3494110 5.1.5.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › WD40 0.51 42.0 2.76e-01 86.6% 39.4%
3259989 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.50 43.0 4.30e-01 94.5% 96.3%
4973090 330.2.1.0 ↗ a+b two layers › dsRBD-like › Ribosome binding protein Y (YfiA homologue) › Ribosome binding protein Y (YfiA homologue) 0.50 36.0 3.98e-01 95.3% 96.0%