←Back to structures

MH153807.1__AWN04079.1__PBI_PEREGRIN_254__00240

Bact-Vir

MH153807.1__AWN04079.1__PBI_PEREGRIN_254__00240

Identity

Accession:
MH153807 ↗
Kingdom:
phage

Quality

74.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Weaselvirus› Rhodococcus_phage_Peregrin

TaxID: 2182361

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 6-88
PDB
Domain cluster: representative
CATH (38)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2ffgA00 3.30.720.20 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › Protein of unknown function DUF1797 0.76 52.0 5.36e-01 80.7% 73.8%
2ychA03 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.68 48.0 4.25e-01 73.5% 95.0%
3mdqA02 3.30.420.150 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Exopolyphosphatase. Domain 2 0.65 49.0 3.73e-01 79.5% 83.6%
3hrgA02 3.30.420.260 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Protein of unknown function DUF3822, C-terminal domain 0.64 47.0 4.28e-01 78.3% 68.4%
4x30A02 2.30.39.10 Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 0.63 44.0 3.58e-01 71.1% 70.8%
6yfiB01 3.30.380.10 Alpha Beta › 2-Layer Sandwich › MS2 Viral Coat Protein › MS2 Viral Coat Protein 0.62 47.0 4.01e-01 80.7% 71.1%
8gtyA02 3.30.420.150 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Exopolyphosphatase. Domain 2 0.61 46.0 3.65e-01 79.5% 82.1%
2kr0A01 2.30.29.70 Mainly Beta › Roll › PH-domain like › Proteasomal ubiquitin receptor Rpn13/ADRM1 0.61 55.0 4.94e-01 100.0% 94.7%
2aq5A01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.61 47.0 3.06e-01 100.0% 19.7%
3nuwA01 3.30.420.300 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 2-keto-3-deoxy-galactonokinase, substrate binding domain 0.61 48.0 4.66e-01 84.3% 98.9%
5eoxB03 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.61 49.0 4.21e-01 86.7% 94.5%
3cm1A00 2.30.31.20 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Sporulation-specific cell division protein SsgB 0.60 54.0 4.60e-01 100.0% 80.1%
3s6pA03 2.60.270.70 Mainly Beta › Sandwich › Mutm (Fpg) Protein; Chain: A, domain 2 › 0.60 47.0 3.94e-01 84.3% 57.7%
4a2bA03 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.60 50.0 4.82e-01 92.8% 92.6%
3ap9A00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.59 50.0 4.17e-01 95.2% 70.9%
1t6cA02 3.30.420.150 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Exopolyphosphatase. Domain 2 0.58 45.0 3.49e-01 83.1% 89.0%
1mgpA02 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.57 47.0 4.18e-01 90.4% 92.6%
3wt0A02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.57 47.0 3.78e-01 89.2% 92.5%
5iroD00 2.60.40.3530 Mainly Beta › Sandwich › Immunoglobulin-like › 0.56 43.0 4.04e-01 83.1% 82.4%
3i8tA00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.56 48.0 4.05e-01 95.2% 74.3%
6e20A00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.56 48.0 4.12e-01 95.2% 77.3%
3flpA00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.56 48.0 3.61e-01 97.6% 78.8%
2z4hA01 2.40.128.300 Mainly Beta › Beta Barrel › Lipocalin › NlpE, N-terminal domain 0.56 47.0 4.87e-01 96.4% 97.5%
2wxwA01 2.30.39.10 Mainly Beta › Roll › Alpha-1-antitrypsin; domain 1 › Alpha-1-antitrypsin, domain 1 0.56 38.0 3.08e-01 71.1% 76.6%
4ebgA00 3.10.450.560 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.55 43.0 4.10e-01 97.6% 72.2%
4hwmA00 2.40.128.500 Mainly Beta › Beta Barrel › Lipocalin › YedD-like protein 0.55 47.0 4.13e-01 91.6% 67.5%
8aimG01 3.10.450.20 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › Bacteriophage PBS2, uracil-glycosylase inhibitor 0.55 38.0 3.89e-01 72.3% 77.8%
1gbgA00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.55 47.0 3.50e-01 95.2% 57.5%
1b9vA00 2.120.10.10 Mainly Beta › 6 Propeller › Neuraminidase › 0.54 48.0 3.12e-01 98.8% 37.2%
3lhnA00 2.40.128.640 Mainly Beta › Beta Barrel › Lipocalin › 0.54 46.0 4.23e-01 94.0% 86.9%
1wi1A01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.54 47.0 4.29e-01 97.6% 91.9%
5dzeA00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.54 48.0 3.64e-01 98.8% 64.3%
1ci3M02 2.40.50.100 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › RNA polymerase II/Efflux pump adaptor protein, barrel-sandwich hybrid domain 0.54 34.0 3.89e-01 72.3% 89.7%
8gzhC01 3.90.1110.10 Alpha Beta › Alpha-Beta Complex › Dna-directed Rna Polymerase Ii 140kd Polypeptide; Chain: B; domain 3 › RNA polymerase Rpb2, domain 2 0.53 47.0 3.68e-01 100.0% 82.9%
7t8tA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.53 46.0 4.03e-01 98.8% 90.1%
5hy7B02 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.52 46.0 3.12e-01 100.0% 33.1%
1h4iA00 2.140.10.10 Mainly Beta › 8 Propeller › Methanol Dehydrogenase; Chain A › Quinoprotein alcohol dehydrogenase-like superfamily 0.51 44.0 2.67e-01 100.0% 40.3%
2f2hA01 2.60.40.1760 Mainly Beta › Sandwich › Immunoglobulin-like › glycosyl hydrolase (family 31) 0.50 39.0 2.74e-01 83.1% 27.8%
ECOD (58)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3302660 109.4.1.1256 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR, PPR_2, PPR_3 0.72 52.0 3.81e-01 77.1% 28.6%
1789440 2484.1.1.61 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › PilM_2 0.70 51.0 3.96e-01 77.1% 73.2%
3890276 4099.1.1.0 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like 0.68 53.0 5.42e-01 81.9% 85.0%
3288144 244.3.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › SufE/NifU › SufE/NifU 0.67 60.0 5.72e-01 97.6% 100.0%
4196676 2484.1.1.174 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › UvrC_RNaseH 0.66 46.0 4.36e-01 72.3% 83.0%
4675215 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.66 46.0 4.28e-01 73.5% 71.4%
5062114 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.65 53.0 4.58e-01 86.7% 94.4%
5048501 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.65 53.0 4.20e-01 88.0% 73.3%
5074822 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.65 51.0 4.39e-01 90.4% 55.2%
4933350 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.64 53.0 4.52e-01 88.0% 57.0%
4976249 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.63 51.0 4.57e-01 86.7% 62.6%
3400912 868.1.1.3 ↗ a+b complex topology › mRNA triphosphatase CET1-related › mRNA triphosphatase CET1-related › mRNA triphosphatase CET1-related › Med20 0.63 49.0 3.59e-01 91.6% 31.4%
3638300 220.1.1.95 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › VID27_PH 0.63 56.0 4.71e-01 100.0% 82.9%
5081740 2484.1.1.342 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › PF29288 0.63 51.0 4.05e-01 88.0% 87.9%
4988335 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.62 50.0 4.35e-01 86.7% 97.6%
5022396 3459.1.1.0 ↗ beta sandwiches › Fas apoptotic inhibitory molecule › Fas apoptotic inhibitory molecule › Fas apoptotic inhibitory molecule 0.62 54.0 5.50e-01 98.8% 98.8%
3388151 2484.1.1.29 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Ppx-GppA 0.62 46.0 3.60e-01 78.3% 85.9%
5001446 2484.1.1.139 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF429 0.61 47.0 3.54e-01 80.7% 57.9%
3966577 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.61 49.0 3.90e-01 86.7% 76.5%
5040575 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.61 50.0 4.41e-01 88.0% 97.5%
3587764 2484.1.1.70 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FtsA 0.61 51.0 3.90e-01 90.4% 79.5%
185116 295.1.1.2 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › SsgA 0.60 54.0 4.59e-01 100.0% 79.6%
4969308 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.60 50.0 4.48e-01 90.4% 98.3%
3532192 220.1.1.1 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH 0.59 52.0 4.64e-01 100.0% 96.7%
3269812 220.1.1.83 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › VID27_N 0.59 52.0 4.17e-01 100.0% 89.4%
1551409 2484.1.1.70 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FtsA 0.58 46.0 3.57e-01 86.7% 78.6%
4926778 861.1.1.3 ↗ a+b two layers › Mago nashi protein › Mago nashi protein › Mago nashi protein › DUF6438 0.58 43.0 3.74e-01 78.3% 99.2%
3733265 4075.1.1.2 ↗ a+b complex topology › RGC domain › RGC domain › RGC domain › PF29130 0.57 51.0 4.73e-01 100.0% 97.1%
3788141 330.1.1.1 ↗ a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.57 38.0 4.00e-01 71.1% 73.3%
3708150 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.57 53.0 3.37e-01 100.0% 24.6%
3255777 4075.1.1.2 ↗ a+b complex topology › RGC domain › RGC domain › RGC domain › PF29130 0.57 50.0 4.87e-01 100.0% 100.0%
3739384 4075.1.1.2 ↗ a+b complex topology › RGC domain › RGC domain › RGC domain › PF29130 0.57 50.0 4.72e-01 98.8% 99.0%
3743052 5.1.4.78 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › TFIIIC_delta 0.57 51.0 3.19e-01 100.0% 26.0%
3851887 10.1.1.4 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Gal-bind_lectin 0.57 48.0 3.89e-01 94.0% 65.0%
3928299 10.1.1.17 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Laminin_G_2 0.57 48.0 3.86e-01 95.2% 63.5%
4191047 2484.1.1.245 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › SHS2_FTSA, PilM_2, FtsA 0.56 49.0 3.15e-01 95.2% 85.7%
4041226 2484.1.1.263 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › SHS2_FTSA, EutA, FtsA 0.56 50.0 3.24e-01 98.8% 86.8%
3469155 719.1.1.0 ↗ beta barrels › XRCC4, N-terminal domain-like › XRCC4, N-terminal domain › XRCC4, N-terminal domain 0.56 43.0 3.88e-01 84.3% 87.5%
4623194 2484.1.1.70 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FtsA 0.56 49.0 3.57e-01 95.2% 69.5%
3264756 4075.1.1.2 ↗ a+b complex topology › RGC domain › RGC domain › RGC domain › PF29130 0.56 49.0 4.68e-01 100.0% 96.0%
3510681 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.56 46.0 4.81e-01 95.2% 97.3%
5063325 2484.1.1.29 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Ppx-GppA 0.56 43.0 3.39e-01 83.1% 90.0%
3660933 10.1.1.11 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Glyco_hydro_16 0.55 48.0 3.62e-01 98.8% 62.9%
3794752 5.1.3.222 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Beta-prop_LRRK2 0.55 50.0 3.16e-01 100.0% 20.7%
3517194 109.54.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › C-terminal tetramerization domain of Utp1/Utp21/Utp12/Utp13 › C-terminal tetramerization domain of Utp1/Utp21/Utp12/Utp13 0.54 49.0 3.03e-01 100.0% 19.2%
4032204 2484.1.1.178 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › SHS2_FTSA+FtsA 0.54 47.0 3.03e-01 95.2% 85.5%
3716329 295.1.1.0 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain 0.54 49.0 3.90e-01 100.0% 59.4%
3942742 2484.1.1.70 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › FtsA 0.53 45.0 3.64e-01 91.6% 74.7%
3595152 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.53 48.0 3.74e-01 100.0% 53.1%
3387779 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.53 38.0 3.40e-01 78.3% 78.3%
3995339 10.1.1.0 ↗ beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases 0.52 46.0 3.86e-01 100.0% 55.3%
4929818 861.1.1.0 ↗ a+b two layers › Mago nashi protein › Mago nashi protein › Mago nashi protein 0.52 46.0 3.92e-01 96.4% 96.3%
3720627 5.1.4.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.52 47.0 3.01e-01 100.0% 24.7%
3194649 5.1.4.37 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › Nup160 0.52 47.0 2.79e-01 100.0% 32.6%
4964626 101.1.2.931 ↗ alpha arrays › HTH › HTH › winged helix domain › DUF7528 0.52 45.0 3.89e-01 95.2% 63.8%
3926057 5.1.5.75 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › WD40, ANAPC4_WD40 0.52 47.0 3.10e-01 100.0% 28.3%
3293481 861.1.1.1 ↗ a+b two layers › Mago nashi protein › Mago nashi protein › Mago nashi protein › Mago_nashi 0.51 45.0 3.89e-01 96.4% 100.0%
3470076 861.1.1.0 ↗ a+b two layers › Mago nashi protein › Mago nashi protein › Mago nashi protein 0.50 44.0 3.70e-01 96.4% 90.7%