←Back to structures

NC_055037.1__YP_010083103.1__KMD26_gp57__00057

Bact-Vir

NC_055037.1__YP_010083103.1__KMD26_gp57__00057

Identity

Accession:
NC_055037 ↗
Kingdom:
phage

Quality

82.6 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Seongbukvirus› Leuconostoc_phage_phiMH1

TaxID: 912321

Cluster

View cluster (2 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 high residues 2-70
PDB
Domain cluster: rep: OP172783.1__WAX12753.1__EC99P2_00056__00056__D2-62
CATH (35)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1vwxT01 2.30.30.70 Mainly Beta › Roll › SH3 type barrels. › Ribosomal protein L21 0.65 37.0 3.35e-01 79.7% 39.2%
2k4vA00 3.30.160.370 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Domain of unknown function DUF5064 0.64 48.0 4.05e-01 92.8% 46.4%
4gnxC03 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.63 54.0 4.09e-01 100.0% 71.0%
4htgA03 3.30.160.40 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain 0.62 44.0 4.31e-01 100.0% 67.1%
3cyjA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.62 54.0 4.51e-01 100.0% 91.0%
1xkzC00 3.40.710.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-lactamase › DD-peptidase/beta-lactamase superfamily 0.61 46.0 3.27e-01 98.6% 23.8%
4ec6A00 3.10.450.540 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.61 44.0 3.77e-01 91.3% 47.7%
7pkwA01 3.10.450.540 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.61 40.0 3.53e-01 84.1% 44.7%
3iq2A00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.61 51.0 4.33e-01 97.1% 86.2%
4p2iA00 3.30.1520.10 Alpha Beta › 2-Layer Sandwich › PX Domain › Phox-like domain 0.61 52.0 4.45e-01 100.0% 95.7%
3ijlA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.61 53.0 4.60e-01 100.0% 100.0%
2chrA01 3.30.390.10 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › Enolase-like, N-terminal domain 0.60 52.0 4.33e-01 100.0% 90.6%
2fggA01 3.30.160.240 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Rv1738 0.60 47.0 4.62e-01 100.0% 81.3%
2hqlA01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.59 48.0 4.39e-01 89.9% 67.0%
3tqmA00 3.30.160.100 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Ribosome hibernation promotion factor-like 0.59 46.0 4.25e-01 97.1% 65.6%
2rqlA00 3.30.160.100 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Ribosome hibernation promotion factor-like 0.59 42.0 3.85e-01 100.0% 55.8%
4ghbA00 2.40.160.190 Mainly Beta › Beta Barrel › Porin › 0.58 39.0 2.75e-01 72.5% 67.5%
1hkgA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.57 44.0 3.69e-01 100.0% 46.2%
8c5yA01 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.57 48.0 3.75e-01 100.0% 78.8%
2zf3C00 2.50.20.30 Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › 0.56 38.0 2.87e-01 98.6% 26.9%
2ddmB00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.55 37.0 2.54e-01 100.0% 17.3%
4rlcA00 2.40.160.20 Mainly Beta › Beta Barrel › Porin › 0.55 47.0 3.87e-01 100.0% 78.5%
2gfgA00 2.40.320.10 Mainly Beta › Beta Barrel › Hypothetical Protein Pfu-838710-001 › Hypothetical Protein Pfu-838710-001 0.55 40.0 2.98e-01 98.6% 28.8%
2gtlN02 2.40.128.620 Mainly Beta › Beta Barrel › Lipocalin › 0.55 45.0 3.54e-01 98.6% 53.5%
7arcC01 3.30.460.80 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › NADH:ubiquinone oxidoreductase Nqo5 subunit 0.54 37.0 3.06e-01 87.0% 36.3%
1oo0A00 3.30.1560.10 Alpha Beta › 2-Layer Sandwich › Mago nashi protein › Mago nashi 0.54 44.0 3.65e-01 98.6% 86.1%
1kyfA01 2.60.40.1230 Mainly Beta › Sandwich › Immunoglobulin-like › Gamma-adaptin ear (GAE) domain 0.54 43.0 3.48e-01 88.4% 64.2%
4akmB00 2.40.160.110 Mainly Beta › Beta Barrel › Porin › 0.53 44.0 3.53e-01 98.6% 82.8%
1ut7B01 2.170.150.80 Mainly Beta › Beta Complex › Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A › NAC domain 0.53 41.0 3.44e-01 95.7% 47.2%
1epaA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.53 38.0 2.98e-01 78.3% 54.4%
3ecrB03 3.30.160.40 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain 0.52 44.0 3.95e-01 98.6% 68.6%
1zc3B00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.52 40.0 3.52e-01 89.9% 54.1%
1n2bB02 3.30.1300.10 Alpha Beta › 2-Layer Sandwich › Pantoate--beta-alanine Ligase; Chain: A,domain 2 › Pantoate-beta-alanine ligase, C-terminal domain 0.52 33.0 2.90e-01 71.0% 41.3%
2qm4A01 2.170.210.10 Mainly Beta › Beta Complex › Dna Repair Protein Xrcc4; Chain: A, domain 1 › DNA double-strand break repair and VJ recombination XRCC4, N-terminal 0.51 43.0 3.46e-01 97.1% 70.6%
4d10F01 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.50 42.0 3.25e-01 100.0% 73.2%
ECOD (54)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4015935 2003.1.2.2 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › GMC_oxred_N 0.76 50.0 3.29e-01 76.8% 16.2%
3413293 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.72 47.0 2.99e-01 85.5% 13.4%
3352475 330.3.1.0 ↗ a+b two layers › dsRBD-like › Peptidyl-tRNA hydrolase domain-like › Peptidyl-tRNA hydrolase domain-like 0.70 59.0 5.81e-01 100.0% 86.7%
4632710 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.67 38.0 4.54e-01 81.2% 86.7%
3887954 10.1.1.72 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › CRLF3_C 0.66 47.0 3.50e-01 92.8% 29.3%
4935679 3414.1.1.13 ↗ beta sandwiches › A putative surface protein › A putative surface protein › A putative surface protein › PF29994 0.65 39.0 3.61e-01 71.0% 45.6%
4012633 277.1.1.0 ↗ a+b two layers › PX domain › PX domain › PX domain 0.65 56.0 4.29e-01 98.6% 83.6%
3726537 2003.1.2.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain 0.65 46.0 2.64e-01 75.4% 42.1%
3749631 4.1.1.14 ↗ beta barrels › SH3 › SH3 › SH3 › Ribosomal_L21e 0.64 38.0 3.32e-01 78.3% 38.1%
3784232 277.1.1.0 ↗ a+b two layers › PX domain › PX domain › PX domain 0.63 54.0 4.25e-01 95.7% 78.6%
3591102 277.1.1.0 ↗ a+b two layers › PX domain › PX domain › PX domain 0.63 55.0 4.34e-01 100.0% 86.0%
5032125 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.63 39.0 2.65e-01 75.4% 16.2%
3587653 243.1.1.0 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.62 45.0 3.72e-01 89.9% 44.2%
167858 218.1.1.1 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › MR_MLE_N 0.62 54.0 4.47e-01 100.0% 89.6%
4929282 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.61 43.0 4.24e-01 95.7% 68.0%
395616 218.1.1.1 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › MR_MLE_N 0.60 51.0 4.39e-01 100.0% 92.4%
4528481 218.1.1.0 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like 0.60 51.0 4.63e-01 100.0% 97.0%
3483729 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.60 49.0 4.22e-01 95.7% 93.3%
3966797 283.2.1.1 ↗ a+b duplicates or obligate multimers › Creatinase/aminopeptidase-like › gpW/gp25-like › gpW/gp25-like › GPW_gp25 0.60 39.0 3.39e-01 89.9% 40.9%
3670792 243.3.1.67 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin › Phytochelatin_C 0.60 36.0 3.67e-01 71.0% 61.5%
3211024 221.13.1.0 ↗ a+b two layers › beta-Grasp › Mitochondrial calcium uniporter N-terminal domain › Mitochondrial calcium uniporter N-terminal domain 0.60 48.0 4.28e-01 100.0% 61.0%
3412668 277.1.1.1 ↗ a+b two layers › PX domain › PX domain › PX domain › PX 0.58 50.0 4.25e-01 100.0% 91.7%
5053966 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.58 40.0 3.76e-01 97.1% 58.8%
4297163 218.1.1.1 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like › MR_MLE_N 0.58 48.0 4.29e-01 98.6% 94.3%
3805925 5.1.3.118 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_3 0.58 48.0 3.16e-01 94.2% 21.7%
4131098 218.1.1.0 ↗ a+b two layers › Enolase-N/ribosomal protein › Enolase N-terminal domain-like › Enolase N-terminal domain-like 0.57 47.0 4.29e-01 97.1% 97.0%
3687369 4.1.1.225 ↗ beta barrels › SH3 › SH3 › SH3 › DUF7025 0.57 42.0 3.73e-01 78.3% 60.0%
3513352 241.15.1.3 ↗ a+b two layers › Type III secretory system chaperone-like › FP (Fbxo7/PI31) dimerization domain › FP (Fbxo7/PI31) dimerization domain › SPC25 0.57 46.0 3.97e-01 100.0% 54.8%
4030981 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.56 39.0 3.79e-01 81.2% 63.7%
5009316 11.1.1.1439 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › PF29294 0.56 45.0 3.33e-01 92.8% 93.2%
3614844 220.1.1.15 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › BBL5 0.56 40.0 3.26e-01 78.3% 38.6%
3177048 719.2.1.0 ↗ beta barrels › XRCC4, N-terminal domain-like › NE0471 N-terminal domain-like › NE0471 N-terminal domain-like 0.55 48.0 4.41e-01 100.0% 100.0%
3276063 210.1.4.1 ↗ a+b four layers › Ntn/PP2C › Ntn › (Glycosyl)asparaginase › Asparaginase_2 0.54 46.0 2.93e-01 100.0% 76.6%
5006387 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.54 47.0 3.56e-01 97.1% 54.1%
4404889 11.1.4.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.54 47.0 3.44e-01 97.1% 47.2%
3600739 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.54 40.0 2.78e-01 79.7% 71.7%
4259027 9.3.1.3 ↗ beta barrels › Lipocalins/Streptavidin › Quinohemoprotein amine dehydrogenase A chain, domain 3-like › Quinohemoprotein amine dehydrogenase A chain, domain 3-like › Eryth_link_C 0.54 46.0 3.91e-01 100.0% 71.5%
3730035 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.54 46.0 4.13e-01 100.0% 100.0%
5049040 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.54 44.0 3.89e-01 95.7% 85.2%
4931364 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.53 38.0 3.55e-01 87.0% 58.9%
3611326 2003.1.3.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Nucleotide-binding domain › DAO 0.53 43.0 2.64e-01 94.2% 59.6%
3507995 2004.1.1.156 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_5 0.53 44.0 3.10e-01 92.8% 97.7%
5057564 213.1.1.0 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) 0.52 36.0 2.84e-01 97.1% 31.2%
3168781 4.1.1.19 ↗ beta barrels › SH3 › SH3 › SH3 › LSM 0.52 36.0 3.21e-01 78.3% 48.6%
3168921 304.48.1.105 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › Peptidase_A2B 0.52 44.0 4.00e-01 100.0% 93.0%
3173885 2484.1.1.307 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Peptidase_A2B 0.51 44.0 3.92e-01 100.0% 88.6%
3969410 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.51 42.0 3.57e-01 100.0% 54.6%
4012953 4.8.1.0 ↗ beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.51 44.0 3.50e-01 100.0% 81.3%
4934542 1.1.1.0 ↗ beta barrels › cradle loop barrel › RIFT-related › acid protease 0.51 43.0 4.05e-01 97.1% 80.0%
3233984 209.1.1.14 ↗ a+b complex topology › C-type lectin-like › C-type lectin-like › C-type lectin-like › PF29411 0.51 37.0 2.69e-01 79.7% 60.7%
3224227 2007.1.2.0 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I 0.50 42.0 2.86e-01 94.2% 79.6%
3806226 708.1.1.1 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain › NAM 0.50 41.0 3.25e-01 95.7% 40.6%
4018672 4.1.1.225 ↗ beta barrels › SH3 › SH3 › SH3 › DUF7025 0.50 40.0 3.40e-01 87.0% 62.6%
4997114 1.1.2.0 ↗ beta barrels › cradle loop barrel › RIFT-related › double psi 0.50 42.0 3.48e-01 100.0% 96.4%