Back to structures

NC_021803.1__YP_008242075.1__Phi13-2_gp050__00050

Bact-Vir

NC_021803.1__YP_008242075.1__Phi13-2_gp050__00050

Identity

Accession:
NC_021803 ↗
Kingdom:
phage

Quality

82.8 mean pLDDT

Cluster

Singleton — not in a non-trivial cluster

3D Structure

Domains

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

D1 high residues 2-44
PDB
Domain cluster: representative
CATH (54)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2zdiB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.80 64.0 4.84e-01 90.7% 36.8%
1fxkC00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.79 68.0 4.79e-01 97.7% 32.3%
4qtcA02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.79 57.0 3.64e-01 79.1% 17.3%
4g6tB00 6.10.20.120 Special › Helix non-globular › Arc Repressor Mutant, subunit A › 0.77 55.0 4.55e-01 74.4% 76.1%
3thxB04 1.10.1420.10 Mainly Alpha › Orthogonal Bundle › MutS, DNA mismatch repair protein; Chain A, domain 3 › 0.76 63.0 4.47e-01 93.0% 32.0%
1uhvA02 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.75 52.0 3.01e-01 72.1% 26.2%
2rdpA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.74 56.0 3.87e-01 81.4% 52.1%
2ckwA03 3.30.70.270 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Reverse transcriptase/Diguanylate cyclase domain 0.74 55.0 3.93e-01 81.4% 29.3%
3pe5A00 3.40.630.190 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › LCP protein 0.73 55.0 3.33e-01 81.4% 22.0%
1fxkB00 1.10.287.370 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.73 57.0 4.36e-01 90.7% 35.8%
1go4A00 3.30.900.10 Alpha Beta › 2-Layer Sandwich › Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A › HORMA domain 0.73 56.0 3.64e-01 86.0% 35.7%
2innB00 1.10.620.20 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase, subunit A › Ribonucleotide Reductase, subunit A 0.72 60.0 3.38e-01 93.0% 20.7%
3qthB00 1.20.120.450 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › dinb family like domain 0.70 57.0 3.92e-01 97.7% 44.5%
5yk4A04 1.10.1420.10 Mainly Alpha › Orthogonal Bundle › MutS, DNA mismatch repair protein; Chain A, domain 3 › 0.70 57.0 3.95e-01 90.7% 29.4%
4fhdA02 3.80.30.30 Alpha Beta › Alpha-Beta Horseshoe › pyruvate-formate lyase- activating enzyme › 0.69 49.0 3.06e-01 74.4% 27.8%
2v3uA01 3.40.190.10 Alpha Beta › 3-Layer(aba) Sandwich › D-Maltodextrin-Binding Protein; domain 2 › Periplasmic binding protein-like II 0.68 47.0 3.20e-01 72.1% 32.7%
1mhyD00 1.10.620.20 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase, subunit A › Ribonucleotide Reductase, subunit A 0.67 58.0 3.27e-01 97.7% 23.1%
6nifA01 3.30.900.10 Alpha Beta › 2-Layer Sandwich › Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A › HORMA domain 0.67 50.0 3.25e-01 83.7% 31.4%
3u1nB01 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.67 54.0 3.16e-01 100.0% 11.6%
2zetC00 3.30.40.10 Alpha Beta › 2-Layer Sandwich › Herpes Virus-1 › Zinc/RING finger domain, C3HC4 (zinc finger) 0.66 52.0 3.72e-01 93.0% 35.5%
3f9uA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.65 53.0 3.66e-01 90.7% 76.6%
4by6D02 1.25.40.800 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.65 47.0 2.95e-01 76.7% 18.2%
7l9pK01 3.30.900.10 Alpha Beta › 2-Layer Sandwich › Cell Cycle, Spindle Assembly Checkpoint Protein; Chain A › HORMA domain 0.65 50.0 3.71e-01 86.0% 31.1%
1dkqA02 3.40.50.1240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Phosphoglycerate mutase-like 0.65 51.0 3.70e-01 88.4% 62.9%
4hhvA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.64 49.0 3.88e-01 88.4% 43.7%
3sfvB02 6.10.140.2010 Special › Helix non-globular › Helix Hairpins › 0.64 53.0 3.47e-01 97.7% 75.5%
2f1rA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.63 37.0 2.59e-01 79.1% 16.2%
1zcdA00 1.20.1530.10 Mainly Alpha › Up-down Bundle › Na+/H+ antiporter like fold › Na+/H+ antiporter like domain 0.63 52.0 3.08e-01 97.7% 85.6%
1d4tA00 3.30.505.10 Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain 0.63 43.0 3.41e-01 76.7% 42.3%
3oqgA00 3.40.1440.50 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › 0.62 43.0 2.85e-01 72.1% 17.6%
4l80D00 3.20.20.60 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Phosphoenolpyruvate-binding domains 0.61 49.0 2.92e-01 97.7% 11.3%
8dvhB01 3.30.230.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.60 42.0 2.73e-01 81.4% 17.9%
4e1pA00 3.30.60.230 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › Lsr2, dimerisation domain 0.60 45.0 4.23e-01 81.4% 70.9%
3e6mA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.60 42.0 3.06e-01 81.4% 50.0%
3wxyA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.58 46.0 3.19e-01 88.4% 64.3%
1vq0A02 3.90.1280.10 Alpha Beta › Alpha-Beta Complex › CBS domain Like › HSP33 redox switch-like 0.57 42.0 3.82e-01 76.7% 61.4%
1pjqA02 3.30.160.110 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Sirohaem synthase, central domain 0.57 40.0 4.31e-01 74.4% 100.0%
2kumA01 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.57 43.0 4.06e-01 88.4% 70.2%
5xyiK00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.56 42.0 3.29e-01 81.4% 100.0%
3vs8H00 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.56 48.0 2.81e-01 100.0% 22.7%
4m7xA01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.56 39.0 3.03e-01 72.1% 41.8%
3mpxA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.56 39.0 3.14e-01 79.1% 38.1%
1xjcA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.55 40.0 2.83e-01 81.4% 36.8%
1z1bA01 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.54 42.0 3.94e-01 88.4% 71.9%
3aleA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.53 39.0 2.74e-01 79.1% 61.5%
5optn00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.53 40.0 3.22e-01 86.0% 51.6%
1i77A00 3.90.10.10 Alpha Beta › Alpha-Beta Complex › Cytochrome C3 › Cytochrome C3 0.53 38.0 2.90e-01 76.7% 67.3%
5ucoA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.53 42.0 2.95e-01 90.7% 61.4%
2y3mA02 3.30.1370.130 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › 0.52 41.0 3.73e-01 81.4% 62.5%
1u0mA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.52 41.0 2.91e-01 88.4% 61.0%
2dmoA00 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.51 33.0 3.00e-01 72.1% 39.7%
2fjrA02 2.10.109.10 Mainly Beta › Ribbon › Umud Fragment, subunit A › Umud Fragment, subunit A 0.51 39.0 3.01e-01 90.7% 76.1%
3euoA02 3.40.47.10 Alpha Beta › 3-Layer(aba) Sandwich › Peroxisomal Thiolase; Chain A, domain 1 › Thiolase/Chalcone synthase 0.51 39.0 2.76e-01 100.0% 24.8%
3ck2A00 3.60.21.10 Alpha Beta › 4-Layer Sandwich › Purple Acid Phosphatase; chain A, domain 2 › Metallo-dependent phosphatases 0.50 38.0 2.72e-01 95.3% 65.5%
ECOD (59)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3740080 109.4.1.548 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TIP120 0.84 54.0 3.19e-01 83.7% 10.0%
4995140 2484.1.1.124 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.84 53.0 3.56e-01 81.4% 19.3%
3214720 192.2.1.1 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.80 67.0 5.20e-01 95.3% 43.2%
3628456 192.2.1.1 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.80 67.0 4.77e-01 95.3% 32.0%
4126575 101.1.2.15 alpha arrays › HTH › HTH › winged helix domain › MarR 0.79 55.0 3.69e-01 100.0% 21.4%
4581682 109.4.1.560 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Mus7 0.79 57.0 3.05e-01 79.1% 3.6%
3599722 109.4.1.548 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TIP120 0.79 54.0 2.84e-01 72.1% 6.7%
3392569 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.78 62.0 4.47e-01 90.7% 31.2%
3598612 220.1.1.230 beta barrels › PH domain-like › PH domain-like › PH domain-like › PF26289 0.78 54.0 4.13e-01 72.1% 98.9%
3254236 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.77 65.0 4.93e-01 97.7% 41.0%
3506058 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.76 65.0 4.97e-01 97.7% 51.0%
5036014 192.2.1.0 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin 0.76 60.0 4.75e-01 90.7% 41.1%
3823652 2500.1.1.2 a/b barrels › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ten stranded beta/alpha barrel › Ribonuc_red_lgC 0.76 56.0 3.10e-01 79.1% 7.4%
4995244 192.2.1.1 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.76 59.0 4.49e-01 90.7% 35.5%
3211768 376.1.1.0 few secondary structure elements › RING/U-box-like › RING/U-box-like › RING/U-box 0.76 57.0 4.31e-01 83.7% 47.6%
3712544 109.4.1.548 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TIP120 0.74 54.0 2.83e-01 100.0% 2.7%
3623035 2004.5.1.3 a/b three-layered sandwiches › P-loop domains-like › Differentially expressed in normal cells and neoplasia (DENN) domain › Differentially expressed in normal cells and neoplasia (DENN) domain › DENN 0.73 56.0 3.45e-01 83.7% 28.0%
4336402 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.73 50.0 3.15e-01 72.1% 47.3%
3742793 601.23.1.4 alpha bundles › Four-helical up-and-down bundle › DNA repair protein MutS, domain III › DNA repair protein MutS, domain III › MutS_IV, MutS_III 0.72 60.0 3.58e-01 93.0% 13.4%
5029669 192.2.1.1 alpha bundles › Long alpha-hairpin › Prefoldin › Prefoldin › Prefoldin_2 0.72 55.0 4.11e-01 90.7% 32.5%
4939406 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.71 54.0 3.53e-01 81.4% 41.7%
3787894 70.3.1.1 beta barrels › beta-clip › SET domain-like › SET domain-like › SET 0.70 61.0 3.57e-01 100.0% 20.0%
3993195 859.1.1.0 a+b two layers › The spindle assembly checkpoint protein mad2 › The spindle assembly checkpoint protein mad2 › The spindle assembly checkpoint protein mad2 0.70 59.0 4.19e-01 95.3% 100.0%
3249581 7512.1.1.6 a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › Glyco_transf_20 0.69 53.0 3.21e-01 81.4% 14.2%
3927940 304.36.1.2 a+b two layers › Alpha-beta plaits › YajQ-like › YajQ-like › RVT_1 0.68 47.0 3.44e-01 72.1% 36.2%
5025927 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.67 48.0 3.70e-01 81.4% 39.1%
3846283 377.1.1.0 few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like 0.66 45.0 4.33e-01 76.7% 62.0%
5032275 101.1.2.15 alpha arrays › HTH › HTH › winged helix domain › MarR 0.66 48.0 3.62e-01 76.7% 78.0%
3999359 101.1.10.0 alpha arrays › HTH › HTH › Cyclin-like 0.66 56.0 4.06e-01 100.0% 59.2%
5030252 101.1.2.48 alpha arrays › HTH › HTH › winged helix domain › PadR 0.65 49.0 3.77e-01 81.4% 76.0%
5069901 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.65 56.0 4.34e-01 95.3% 75.6%
3498304 102.1.3.0 alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › PAP/OAS1 substrate-binding domain 0.64 56.0 3.41e-01 97.7% 17.8%
4629529 2002.1.1.420 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › HpcH_HpaI, PF25918 0.64 55.0 3.17e-01 100.0% 22.1%
3935908 304.48.1.1 a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › RVT_1 0.64 44.0 3.13e-01 72.1% 29.6%
4949735 101.1.2.150 alpha arrays › HTH › HTH › winged helix domain › HTH_45 0.63 48.0 3.87e-01 83.7% 77.6%
5001620 632.1.1.0 alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain 0.63 54.0 4.09e-01 97.7% 99.0%
3607727 109.4.1.548 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TIP120 0.62 55.0 3.02e-01 100.0% 12.6%
3512133 2003.1.1.0 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains 0.61 45.0 2.72e-01 79.1% 77.6%
5013841 101.1.2.14 alpha arrays › HTH › HTH › winged helix domain › HTH_5 0.59 45.0 3.23e-01 83.7% 55.2%
3925496 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.59 46.0 3.65e-01 86.0% 41.1%
3267918 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.59 40.0 3.82e-01 74.4% 69.1%
3929748 109.4.1.1303 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › HAT_PRP39_N, HAT_PRP39_C 0.58 44.0 2.60e-01 81.4% 17.6%
4068860 101.1.2.54 alpha arrays › HTH › HTH › winged helix domain › Penicillinase_R 0.58 48.0 3.55e-01 95.3% 62.5%
5035263 101.1.2.14 alpha arrays › HTH › HTH › winged helix domain › HTH_5 0.58 41.0 3.20e-01 79.1% 73.3%
4022881 300.1.1.0 a+b three layers › Phospholipase D/nuclease › Phospholipase D/nuclease › Phospholipase D/nuclease 0.58 42.0 2.72e-01 88.4% 22.3%
3400082 101.1.2.109 alpha arrays › HTH › HTH › winged helix domain › Rio2_N 0.58 48.0 3.72e-01 95.3% 64.0%
3937387 323.1.1.0 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases 0.57 44.0 3.32e-01 90.7% 80.0%
4243508 101.1.2.14 alpha arrays › HTH › HTH › winged helix domain › HTH_5 0.56 50.0 3.75e-01 100.0% 61.9%
4636695 304.36.1.1 a+b two layers › Alpha-beta plaits › YajQ-like › YajQ-like › DUF520 0.56 39.0 3.32e-01 72.1% 48.5%
4938390 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.56 50.0 3.53e-01 100.0% 51.5%
4127813 327.16.1.3 a+b two layers › Alpha-lytic protease prodomain-like › Ring-building motif II in type III secretion system › Ring-building motif II in type III secretion system › Secretin_N 0.55 45.0 3.42e-01 95.3% 93.6%
4973217 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.55 45.0 3.64e-01 95.3% 75.3%
3755415 2484.1.1.236 mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › PF27940 0.54 47.0 3.04e-01 100.0% 28.6%
4255188 318.1.1.0 a+b two layers › Ribosomal protein L6 › Ribosomal protein L6 › Ribosomal protein L6 0.53 41.0 3.44e-01 97.7% 84.4%
4446502 246.2.1.9 a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › Metallophos_2 0.52 39.0 2.77e-01 88.4% 67.9%
4984339 101.1.2.150 alpha arrays › HTH › HTH › winged helix domain › HTH_45 0.52 41.0 3.42e-01 86.0% 57.3%
5010149 377.1.1.131 few secondary structure elements › Glucocorticoid receptor-like › LIM domain-like › LIM domain-like › TRASH_HVO_1752_C 0.51 33.0 3.46e-01 72.1% 70.0%
3589184 101.1.1.0 alpha arrays › HTH › HTH › Three-helical HTH 0.51 35.0 2.97e-01 74.4% 68.0%
5080529 101.1.2.141 alpha arrays › HTH › HTH › winged helix domain › HTH_24 0.51 39.0 3.12e-01 88.4% 65.3%