←Back to structures

NC_054983.1__YP_010080112.1__KMC71_gp21__00021

Bact-Vir

NC_054983.1__YP_010080112.1__KMC71_gp21__00021

Identity

Accession:
NC_054983 ↗
Kingdom:
phage

Quality

82.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Phietavirus› Staphylococcus_phage_UPMK_2

TaxID: 2029631

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 2-92
PDB
Domain cluster: representative
CATH (49)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2x8kA01 2.40.30.200 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › 0.67 58.0 5.55e-01 95.6% 89.5%
4z85A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.62 55.0 4.30e-01 98.9% 62.4%
2o30A00 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.61 46.0 4.81e-01 94.5% 86.6%
3jr1A01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.60 44.0 4.36e-01 100.0% 72.7%
4p02A03 2.40.10.220 Mainly Beta › Beta Barrel › Thrombin, subunit H › predicted glycosyltransferase like domains 0.60 52.0 4.75e-01 100.0% 73.0%
6fmeA03 2.20.220.10 Mainly Beta › Single Sheet › Glycosyl hydrolase fold › alpha-Amylases 0.60 33.0 4.04e-01 100.0% 82.3%
2vrsA03 2.60.90.40 Mainly Beta › Sandwich › Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) › 0.59 53.0 4.70e-01 100.0% 96.2%
4pbdA00 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.59 48.0 4.60e-01 85.7% 76.5%
4ympA00 2.60.40.1850 Mainly Beta › Sandwich › Immunoglobulin-like › 0.59 46.0 4.27e-01 100.0% 67.0%
3db0B00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.58 51.0 4.68e-01 100.0% 85.5%
2hq9B00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.58 51.0 4.49e-01 100.0% 83.9%
3u5wA00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.58 51.0 4.61e-01 100.0% 81.7%
2aneH00 2.30.130.40 Mainly Beta › Roll › Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 › LON domain-like 0.58 46.0 4.40e-01 89.0% 78.9%
2i02A00 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.57 49.0 4.37e-01 100.0% 79.3%
2iabA01 2.30.110.10 Mainly Beta › Roll › Pnp Oxidase; Chain A › Electron Transport, Fmn-binding Protein; Chain A 0.57 49.0 4.33e-01 100.0% 74.8%
2jiiA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.56 46.0 4.35e-01 100.0% 72.7%
2ewhA01 3.30.70.1710 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › BMC (bacterial microcompartment) domain 0.56 37.0 3.84e-01 81.3% 71.8%
4ioyX01 2.30.29.150 Mainly Beta › Roll › PH-domain like › 0.56 40.0 3.66e-01 75.8% 98.4%
1zc3B00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.56 41.0 3.90e-01 76.9% 91.7%
3n79A01 3.30.70.1710 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › BMC (bacterial microcompartment) domain 0.56 36.0 3.87e-01 84.6% 76.9%
4ci2B02 2.30.130.40 Mainly Beta › Roll › Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 › LON domain-like 0.55 44.0 4.04e-01 89.0% 67.2%
2rgnB02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 40.0 3.67e-01 76.9% 80.5%
1mhmA00 3.60.90.10 Alpha Beta › 4-Layer Sandwich › S-adenosylmethionine decarboxylase › S-adenosylmethionine decarboxylase 0.55 42.0 3.09e-01 100.0% 29.6%
3szeA01 2.40.10.120 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.55 48.0 3.38e-01 100.0% 39.0%
2pmzB07 2.40.50.150 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II, Rpb2 subunit, wall domain 0.55 39.0 3.56e-01 74.7% 89.5%
4odbA00 2.60.90.20 Mainly Beta › Sandwich › Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) › Virus attachment protein , globular domain 0.55 47.0 4.01e-01 100.0% 82.7%
3gs9A01 6.20.110.10 Special › Other non-globular › Thrombin, subunit H › 0.55 43.0 4.54e-01 92.3% 98.7%
7cayA01 2.30.130.40 Mainly Beta › Roll › Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4 › LON domain-like 0.54 41.0 4.06e-01 89.0% 77.0%
1twfB07 2.40.50.150 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II, Rpb2 subunit, wall domain 0.54 39.0 3.54e-01 74.7% 89.5%
8ornD01 2.50.20.10 Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › Lipoprotein localisation LolA/LolB/LppX 0.54 40.0 3.23e-01 78.0% 65.9%
1kkeA02 2.60.90.20 Mainly Beta › Sandwich › Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) › Virus attachment protein , globular domain 0.54 47.0 4.14e-01 100.0% 97.2%
3pg7A02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.54 40.0 3.75e-01 78.0% 85.5%
2wc7A02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.54 40.0 4.32e-01 97.8% 91.1%
1mi1A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.54 37.0 3.60e-01 72.5% 97.1%
3f5rA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.54 39.0 3.66e-01 89.0% 61.9%
5axgA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.53 48.0 4.29e-01 100.0% 98.4%
3dhuA02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.53 40.0 4.43e-01 98.9% 97.3%
4tyzA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.52 38.0 3.59e-01 75.8% 82.6%
2wstA00 2.60.90.10 Mainly Beta › Sandwich › Adenovirus Type 5 Fiber Protein (Receptor Binding Domain) › Adenovirus pIV-related, attachment domain 0.52 45.0 3.73e-01 100.0% 97.7%
1wzaA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.52 41.0 4.41e-01 98.9% 100.0%
4wrnA02 2.60.40.3210 Mainly Beta › Sandwich › Immunoglobulin-like › Zona pellucida, ZP-N domain 0.52 34.0 3.31e-01 93.4% 59.0%
1jyoA00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.52 40.0 3.57e-01 100.0% 57.7%
2wcoA03 2.60.220.10 Mainly Beta › Sandwich › Chondroitinase Ac; Chain A, domain 3 › Polysaccharide lyase family 8-like, C-terminal 0.52 47.0 4.36e-01 100.0% 80.9%
4xb3A03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.51 38.0 4.26e-01 98.9% 100.0%
3mpxA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.51 36.0 3.57e-01 73.6% 87.6%
3edfA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.51 41.0 4.39e-01 100.0% 100.0%
1cgtA02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.51 42.0 4.16e-01 100.0% 87.2%
2zxdA02 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.50 44.0 4.48e-01 98.9% 97.8%
3amkA03 2.60.40.1180 Mainly Beta › Sandwich › Immunoglobulin-like › Golgi alpha-mannosidase II 0.50 46.0 4.46e-01 100.0% 94.0%
ECOD (67)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4995815 1.1.13.0 ↗ beta barrels › cradle loop barrel › RIFT-related › Phage tail proteins 0.68 60.0 5.36e-01 96.7% 77.6%
3660388 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.66 46.0 4.64e-01 86.8% 72.2%
5026297 309.1.2.1 ↗ a+b two layers › LuxS, MPP, ThrRS/AlaRS common domain › LuxS, MPP, ThrRS/AlaRS common domain › ThrRS/AlaRS editing domain › tRNA_SAD 0.64 57.0 4.81e-01 100.0% 92.9%
4934590 319.1.1.0 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones 0.64 48.0 4.72e-01 83.5% 74.7%
4928207 319.1.1.0 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones 0.63 48.0 5.23e-01 80.2% 97.3%
5075917 1.1.5.17 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › DUF447_N 0.62 55.0 4.74e-01 100.0% 80.7%
3611570 206.1.1.87 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase, RIO1 0.62 46.0 3.19e-01 100.0% 24.5%
5013200 1.1.5.17 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel › DUF447_N 0.62 55.0 4.78e-01 100.0% 80.7%
5042256 319.1.1.0 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones 0.62 50.0 4.92e-01 86.8% 84.8%
3709821 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.60 44.0 3.95e-01 75.8% 95.2%
5078655 873.1.1.15 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › PF27323 0.60 55.0 4.69e-01 100.0% 64.1%
4996474 873.1.1.22 ↗ a+b complex topology › H-NOX domain › H-NOX domain › H-NOX domain › PF25939 0.60 55.0 4.30e-01 100.0% 50.0%
2458379 12.1.1.13 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › Suc_Porlyase_C 0.60 33.0 3.79e-01 100.0% 71.8%
3715543 220.1.1.200 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_30 0.59 44.0 4.00e-01 76.9% 91.7%
3247872 11.1.1.843 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF7034 0.59 47.0 4.18e-01 85.7% 60.8%
3685973 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.59 45.0 4.09e-01 85.7% 59.2%
4509138 1.1.9.5 ↗ beta barrels › cradle loop barrel › RIFT-related › PUA domain › LON_substr_bdg 0.59 48.0 3.66e-01 89.0% 38.6%
3283546 1.1.5.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.59 52.0 4.54e-01 100.0% 71.3%
3742788 319.1.1.3 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › CS 0.59 47.0 4.46e-01 84.6% 77.1%
3269789 319.1.1.3 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones › CS 0.58 44.0 4.53e-01 82.4% 84.7%
3583844 220.1.1.30 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_BEACH 0.58 42.0 3.60e-01 76.9% 84.7%
2771336 12.1.1.0 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain 0.58 40.0 4.56e-01 100.0% 98.5%
3598106 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.57 42.0 3.92e-01 76.9% 100.0%
4588052 1.1.9.5 ↗ beta barrels › cradle loop barrel › RIFT-related › PUA domain › LON_substr_bdg 0.57 46.0 3.44e-01 89.0% 34.0%
3407835 1.1.5.0 ↗ beta barrels › cradle loop barrel › RIFT-related › FMN-binding split barrel 0.57 45.0 3.32e-01 98.9% 30.5%
3250619 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.57 42.0 3.96e-01 78.0% 97.3%
3742004 220.1.1.30 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_BEACH 0.57 41.0 3.70e-01 75.8% 87.2%
3232944 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.57 47.0 3.18e-01 100.0% 24.8%
3880252 220.1.1.162 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PF31014 0.56 41.0 3.40e-01 76.9% 80.6%
3777845 633.23.1.17 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › DuoxA 0.56 41.0 2.92e-01 75.8% 32.5%
3899369 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.56 40.0 3.46e-01 76.9% 61.3%
3293992 12.1.1.35 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › Melibiase_C 0.56 50.0 4.89e-01 100.0% 96.0%
3923512 220.1.1.66 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › SOS1_NGEF_PH 0.56 41.0 3.73e-01 76.9% 81.7%
3441915 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 44.0 3.03e-01 100.0% 24.8%
3321290 11.1.1.902 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_GEX2_N 0.55 44.0 4.08e-01 85.7% 70.4%
3529797 220.1.1.68 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_Tiam1 0.55 40.0 3.31e-01 76.9% 77.1%
3888868 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.55 41.0 3.75e-01 78.0% 86.7%
3717655 220.1.1.30 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_BEACH 0.55 40.0 3.94e-01 76.9% 99.0%
3767718 220.1.1.125 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_PLEKHM2 0.55 40.0 3.40e-01 75.8% 72.7%
3615126 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.55 40.0 3.27e-01 75.8% 76.4%
3701631 220.1.1.200 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_30 0.55 41.0 3.75e-01 80.2% 92.0%
4030718 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.55 40.0 3.67e-01 76.9% 95.0%
3266298 220.1.1.8 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.55 40.0 3.51e-01 76.9% 73.9%
3587162 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.54 40.0 3.35e-01 76.9% 69.3%
3536412 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.54 40.0 3.46e-01 76.9% 71.4%
3626506 220.1.1.66 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › SOS1_NGEF_PH 0.54 40.0 3.48e-01 78.0% 78.6%
3686517 220.1.1.112 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_10 0.54 39.0 3.26e-01 76.9% 73.9%
3405822 220.1.1.43 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › SIN1_PH 0.54 40.0 3.47e-01 79.1% 75.9%
3600173 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.54 39.0 3.09e-01 76.9% 78.5%
3371896 11.1.1.122 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › GO-like_E_set 0.54 43.0 3.95e-01 85.7% 67.2%
3930773 633.23.1.17 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › DuoxA 0.54 39.0 2.79e-01 75.8% 35.2%
3242949 633.23.1.17 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › DuoxA 0.53 38.0 2.74e-01 74.7% 35.1%
3875149 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.53 38.0 3.59e-01 76.9% 83.5%
3605574 319.1.1.0 ↗ beta sandwiches › HSP20-like › HSP20-like chaperones › HSP20-like chaperones 0.53 46.0 3.78e-01 100.0% 57.1%
4567929 5.1.4.169 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Beta-prop_RSE1_2nd 0.52 34.0 2.30e-01 75.8% 16.5%
3536413 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.52 38.0 3.62e-01 76.9% 87.3%
3542022 220.1.1.115 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_19 0.52 38.0 3.21e-01 78.0% 77.4%
3263571 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.52 38.0 3.05e-01 76.9% 60.0%
3540139 220.1.1.79 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › TBC1D23_C 0.51 38.0 3.48e-01 78.0% 85.8%
3998992 220.1.1.79 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › TBC1D23_C 0.51 38.0 3.34e-01 78.0% 90.4%
3789630 633.23.1.0 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin 0.51 35.0 2.67e-01 71.4% 75.7%
1972 12.1.1.16 ↗ beta sandwiches › Glycosyl hydrolase domain-like › Glycosyl hydrolase domain › Glycosyl hydrolase domain › Cyc-maltodext_C 0.51 41.0 4.37e-01 100.0% 97.6%
3788003 220.1.1.112 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_10 0.51 37.0 3.23e-01 76.9% 77.2%
3915831 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.51 38.0 3.43e-01 79.1% 76.8%
3547918 11.1.1.2 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › fn3 0.50 39.0 3.36e-01 82.4% 64.3%
3250882 220.1.1.199 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_NISCH_C 0.50 37.0 3.17e-01 76.9% 81.2%
3344768 241.6.1.0 ↗ a+b two layers › Type III secretory system chaperone-like › Arp2/3 complex subunits › Arp2/3 complex subunits 0.50 39.0 3.61e-01 100.0% 65.5%