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MK016502.1__AYR00155.1__PBI_PAT3_38__00038

Bact-Vir

MK016502.1__AYR00155.1__PBI_PAT3_38__00038

Identity

Accession:
MK016502 ↗
Kingdom:
phage

Quality

88.3 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Kostyavirus› Mycobacterium_phage_Pat3

TaxID: 2484214

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 medium residues 3-56
PDB
Domain cluster: representative
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2ap1A01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.63 47.0 3.55e-01 81.5% 86.3%
4o1nD01 3.10.20.120 Alpha Beta › Roll › Ubiquitin-like (UB roll) › 0.63 47.0 3.80e-01 83.3% 83.5%
3hrgA02 3.30.420.260 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Protein of unknown function DUF3822, C-terminal domain 0.61 45.0 3.61e-01 81.5% 73.7%
3oqgA00 3.40.1440.50 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › 0.60 45.0 3.17e-01 79.6% 37.5%
2gupA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.59 42.0 3.51e-01 75.9% 49.5%
2nrhB02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.59 42.0 3.15e-01 77.8% 67.4%
1yd0A00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.58 43.0 3.74e-01 81.5% 57.3%
1mzpA01 3.30.190.20 Alpha Beta › 2-Layer Sandwich › Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase › Ribosomal protein L1/L10, rRNA-binding domain 0.58 43.0 3.35e-01 81.5% 65.9%
3h1qA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.58 42.0 3.35e-01 77.8% 73.9%
7x3hA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.58 43.0 3.42e-01 81.5% 75.9%
2h3gX01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.57 41.0 3.55e-01 77.8% 60.2%
2vzwB00 3.30.450.40 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › GAF domain 0.57 40.0 3.08e-01 79.6% 83.9%
3djcB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.56 40.0 3.53e-01 77.8% 60.2%
1y13A00 3.30.479.10 Alpha Beta › 2-Layer Sandwich › Tetrahydropterin Synthase; Chain A › 6-pyruvoyl tetrahydropterin synthase/QueD 0.55 44.0 3.25e-01 92.6% 92.6%
8gtyA02 3.30.420.150 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Exopolyphosphatase. Domain 2 0.55 38.0 2.79e-01 75.9% 83.2%
2p1jA01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.55 39.0 3.02e-01 79.6% 49.3%
2a74A05 2.60.40.1930 Mainly Beta › Sandwich › Immunoglobulin-like › Macroglobulin (MG2) domain 0.55 41.0 3.30e-01 81.5% 45.7%
1n6zA00 3.10.20.250 Alpha Beta › Roll › Ubiquitin-like (UB roll) › YML108W-like 0.54 41.0 3.47e-01 88.9% 80.0%
8oqkA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.54 39.0 3.31e-01 81.5% 87.4%
6dxwA01 3.60.60.10 Alpha Beta › 4-Layer Sandwich › Penicillin V Acylase; Chain A › Penicillin V Acylase; Chain A 0.54 40.0 2.71e-01 81.5% 36.2%
4h4nA00 2.60.40.3750 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 40.0 3.87e-01 83.3% 74.2%
2jkgA00 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.53 38.0 2.89e-01 83.3% 44.2%
3m70A01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.53 36.0 2.99e-01 83.3% 37.7%
2xheA03 3.90.830.10 Alpha Beta › Alpha-Beta Complex › Syntaxin Binding Protein 1; Chain A, domain 2 › Sec1/Munc18 (SM) protein, domain 3a 0.52 38.0 3.01e-01 79.6% 82.6%
2yocA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.52 37.0 3.02e-01 77.8% 54.6%
3eipA00 3.10.50.20 Alpha Beta › Roll › Chitinase A; domain 3 › Cloacin immunity protein 0.52 35.0 3.15e-01 74.1% 95.2%
2yx6D01 3.30.420.130 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Dinitrogenase iron-molybdenum cofactor biosynthesis domain 0.51 42.0 3.52e-01 98.1% 82.4%
4mt1A07 3.30.70.1440 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Multidrug efflux transporter AcrB pore domain 0.50 35.0 2.96e-01 75.9% 87.3%
3gzkA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.50 37.0 3.33e-01 81.5% 59.5%
1mdbA02 3.40.50.980 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.50 35.0 2.57e-01 74.1% 43.7%
1ze3D00 3.10.20.410 Alpha Beta › Roll › Ubiquitin-like (UB roll) › PapC, N-terminal domain 0.50 37.0 3.02e-01 81.5% 69.8%
4rpoA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.50 37.0 3.02e-01 85.2% 52.5%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3957585 2484.1.1.144 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DEDD_Tnp_IS110 0.64 47.0 4.00e-01 81.5% 89.5%
4976249 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.63 46.0 3.68e-01 81.5% 84.3%
3589909 2484.1.1.144 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DEDD_Tnp_IS110 0.63 46.0 3.63e-01 81.5% 77.5%
5022939 2484.1.1.23 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Hydantoinase_A 0.60 44.0 3.48e-01 81.5% 86.7%
None — 0.59 42.0 3.03e-01 77.8% 59.4%
5070409 821.1.1.0 ↗ a+b three layers › GIY-YIG endonuclease › GIY-YIG endonuclease › GIY-YIG endonuclease 0.59 43.0 3.74e-01 79.6% 56.8%
3290579 221.10.1.1 ↗ a+b two layers › beta-Grasp › FdhD/NarQ beta-grasp fold domain › FdhD/NarQ beta-grasp fold domain › FdhD-NarQ 0.59 43.0 3.90e-01 79.6% 85.3%
4989862 221.10.1.1 ↗ a+b two layers › beta-Grasp › FdhD/NarQ beta-grasp fold domain › FdhD/NarQ beta-grasp fold domain › FdhD-NarQ 0.59 44.0 4.13e-01 85.2% 92.9%
3191646 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.58 42.0 4.13e-01 79.6% 81.7%
4989260 221.10.1.1 ↗ a+b two layers › beta-Grasp › FdhD/NarQ beta-grasp fold domain › FdhD/NarQ beta-grasp fold domain › FdhD-NarQ 0.58 44.0 4.17e-01 83.3% 83.1%
4033864 221.10.1.1 ↗ a+b two layers › beta-Grasp › FdhD/NarQ beta-grasp fold domain › FdhD/NarQ beta-grasp fold domain › FdhD-NarQ 0.58 43.0 4.13e-01 83.3% 87.7%
3687767 4121.1.1.7 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › PF26616 0.58 44.0 2.65e-01 87.0% 45.1%
5067321 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.58 43.0 3.71e-01 83.3% 85.6%
4934332 4004.1.1.3 ↗ beta sandwiches › NAD kinase beta sandwich domain-like › NAD kinase beta sandwich domain-like › NAD kinase beta sandwich domain-like › NAD_kinase_C 0.57 44.0 3.13e-01 83.3% 48.1%
4980279 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.57 39.0 3.70e-01 74.1% 91.4%
4141802 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.57 42.0 3.33e-01 81.5% 86.7%
4290748 223.1.1.3 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › GAF 0.57 40.0 2.85e-01 79.6% 63.0%
4004704 3115.6.1.2 ↗ a+b two layers › GP2-like › Bacterial RNA polymerase subunit epsilon › Bacterial RNA polymerase subunit epsilon › PF28597 0.56 39.0 4.16e-01 79.6% 88.9%
4052313 2484.1.1.10 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › TsaD 0.56 41.0 3.40e-01 81.5% 87.6%
3929985 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.56 39.0 3.31e-01 75.9% 55.0%
3210917 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.56 42.0 3.66e-01 83.3% 62.4%
4471876 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.56 39.0 3.16e-01 77.8% 82.5%
4967731 221.10.1.1 ↗ a+b two layers › beta-Grasp › FdhD/NarQ beta-grasp fold domain › FdhD/NarQ beta-grasp fold domain › FdhD-NarQ 0.55 41.0 3.94e-01 83.3% 89.2%
4226504 221.10.1.1 ↗ a+b two layers › beta-Grasp › FdhD/NarQ beta-grasp fold domain › FdhD/NarQ beta-grasp fold domain › FdhD-NarQ 0.55 42.0 3.69e-01 88.9% 87.8%
5063665 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.55 34.0 3.62e-01 88.9% 73.3%
3897274 284.1.1.12 ↗ a+b two layers › FKBP-like › FKBP-like › FKBP-like › TR61B_FKBP-like 0.54 40.0 3.78e-01 83.3% 90.0%
4229347 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.54 39.0 3.17e-01 77.8% 80.9%
5015864 221.10.1.1 ↗ a+b two layers › beta-Grasp › FdhD/NarQ beta-grasp fold domain › FdhD/NarQ beta-grasp fold domain › FdhD-NarQ 0.54 42.0 3.66e-01 87.0% 90.6%
4480622 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.54 38.0 2.94e-01 75.9% 65.1%
4951383 221.10.1.1 ↗ a+b two layers › beta-Grasp › FdhD/NarQ beta-grasp fold domain › FdhD/NarQ beta-grasp fold domain › FdhD-NarQ 0.54 41.0 3.72e-01 88.9% 93.8%
5071156 3714.1.1.1 ↗ a+b two layers › Lon-like protease MtaLonC helical domain › Lon-like protease MtaLonC helical domain › Lon-like protease MtaLonC helical domain › LonC_helical 0.54 36.0 2.50e-01 70.4% 96.0%
5005723 223.1.1.14 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains › PAS_4 0.53 37.0 2.41e-01 74.1% 28.2%
3331184 7579.1.1.14 ↗ a/b three-layered sandwiches › alpha/beta-Hydrolases › alpha/beta-Hydrolases › alpha/beta-Hydrolases › Lipase_3 0.52 37.0 2.52e-01 81.5% 31.0%
4966253 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.52 38.0 3.25e-01 81.5% 57.9%
4091244 2484.1.1.37 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Pan_kinase 0.52 36.0 2.92e-01 77.8% 42.4%
5081200 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.52 37.0 3.59e-01 72.2% 66.7%
4970388 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.52 36.0 3.35e-01 77.8% 97.3%
4998579 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.51 37.0 2.71e-01 87.0% 49.7%
5038458 4076.4.1.0 ↗ a+b two layers › L9 N-domain-like › primase chain A, C-terminal domain › primase chain A, C-terminal domain 0.50 31.0 3.18e-01 83.3% 64.0%