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NC_004914.3__NP_859377.1__Stx2II_p130__00131

Bact-Vir

NC_004914.3__NP_859377.1__Stx2II_p130__00131

Identity

Accession:
NC_004914 ↗
Kingdom:
phage

Quality

74.3 mean pLDDT

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 23-69
PDB
CATH (52)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2l2mA00 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.81 69.0 6.06e-01 95.7% 75.7%
7pikC01 3.30.420.10 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › Ribonuclease H-like superfamily/Ribonuclease H 0.77 67.0 4.36e-01 100.0% 97.6%
2kvtA00 3.30.730.30 Alpha Beta › 2-Layer Sandwich › GCC-box Binding Domain › YaiA protein 0.76 63.0 5.67e-01 100.0% 74.6%
3c4bA02 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.73 63.0 5.69e-01 100.0% 77.6%
1mgpA02 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.70 59.0 4.46e-01 100.0% 45.5%
3fgbA00 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.68 49.0 2.96e-01 78.7% 20.6%
2yztA00 3.30.160.250 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.68 55.0 5.06e-01 100.0% 69.7%
3htxA01 3.30.160.20 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.67 55.0 4.77e-01 93.6% 76.3%
2nmlA00 3.30.2260.10 Alpha Beta › 2-Layer Sandwich › ERH-like fold › Enhancer of rudimentary 0.67 47.0 3.72e-01 74.5% 39.0%
3lxqA01 3.30.1120.80 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.67 43.0 3.43e-01 72.3% 31.3%
1nioA01 3.40.420.10 Alpha Beta › 3-Layer(aba) Sandwich › Ricin (A subunit); domain 1 › Ricin (A subunit), domain 1 0.66 55.0 3.80e-01 93.6% 29.0%
2k7iA01 3.30.160.160 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › YegP-like 0.66 52.0 5.27e-01 100.0% 93.8%
4za3A01 3.40.420.10 Alpha Beta › 3-Layer(aba) Sandwich › Ricin (A subunit); domain 1 › Ricin (A subunit), domain 1 0.66 53.0 3.70e-01 95.7% 26.4%
2dt8A02 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.66 54.0 4.07e-01 100.0% 49.2%
1x0tA02 6.20.50.20 Special › Other non-globular › N-terminal domain of TfIIb › 0.65 41.0 4.15e-01 72.3% 64.4%
2bn8A00 3.30.730.20 Alpha Beta › 2-Layer Sandwich › GCC-box Binding Domain › Cell division activator CedA 0.64 51.0 4.62e-01 97.9% 64.2%
1pzxA03 3.30.1180.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein Tm841; Chain: A;domain 3 › 0.63 53.0 4.06e-01 100.0% 44.3%
1zvfB01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.63 51.0 3.68e-01 100.0% 68.3%
3f6gA01 3.30.160.740 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.63 52.0 4.99e-01 100.0% 84.5%
5nfiB02 2.60.40.2090 Mainly Beta › Sandwich › Immunoglobulin-like › 0.63 53.0 3.93e-01 100.0% 76.7%
3kxyJ00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.62 51.0 3.88e-01 100.0% 69.8%
1nqzA00 3.90.79.10 Alpha Beta › Alpha-Beta Complex › Nucleoside Triphosphate Pyrophosphohydrolase › Nucleoside Triphosphate Pyrophosphohydrolase 0.62 46.0 3.16e-01 89.4% 22.8%
4qdgA02 2.60.40.2090 Mainly Beta › Sandwich › Immunoglobulin-like › 0.60 50.0 3.73e-01 100.0% 71.9%
3r7wB02 3.30.450.190 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.60 48.0 3.76e-01 100.0% 42.4%
2hc5A01 3.30.160.170 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › FlaG-like 0.60 47.0 3.81e-01 93.6% 43.9%
4hslA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.59 47.0 3.42e-01 100.0% 65.7%
3payB02 2.60.40.2090 Mainly Beta › Sandwich › Immunoglobulin-like › 0.58 48.0 3.59e-01 97.9% 68.2%
1z1bA01 3.30.160.60 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Classic Zinc Finger 0.58 47.0 4.51e-01 97.9% 86.0%
1xkiA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.58 40.0 2.97e-01 72.3% 32.0%
2z0qA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.58 50.0 3.71e-01 100.0% 47.7%
1qh5A00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.57 46.0 2.93e-01 93.6% 46.9%
2lstA00 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.57 45.0 3.51e-01 100.0% 77.7%
1m2xA00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.57 44.0 2.95e-01 91.5% 36.1%
3lxrF00 1.10.4120.20 Mainly Alpha › Orthogonal Bundle › SopE-like GEF fold › 0.56 47.0 3.19e-01 95.7% 79.0%
3aqoA02 3.30.1360.200 Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 › 0.56 47.0 3.46e-01 97.9% 57.4%
4xq7A01 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.56 40.0 2.81e-01 100.0% 23.1%
2h1eA02 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.56 46.0 4.41e-01 93.6% 81.8%
1xm8A00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.56 46.0 2.93e-01 95.7% 40.9%
7byjA02 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.56 46.0 3.69e-01 100.0% 46.3%
3h04A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.56 48.0 2.97e-01 97.9% 92.6%
1a15A00 2.40.50.40 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.55 40.0 3.61e-01 76.6% 56.7%
4dt4A02 2.40.10.330 Mainly Beta › Beta Barrel › Thrombin, subunit H › 0.55 37.0 3.57e-01 80.9% 59.6%
2v8qA01 3.30.310.80 Alpha Beta › 2-Layer Sandwich › TATA-Binding Protein › Kinase associated domain 1, KA1 0.54 38.0 3.10e-01 89.4% 39.3%
3wknF00 6.20.50.120 Special › Other non-globular › N-terminal domain of TfIIb › 0.53 36.0 3.64e-01 74.5% 71.7%
1sjgA00 2.102.10.10 Mainly Beta › 3-layer Sandwich › Rieske Iron-sulfur Protein › Rieske [2Fe-2S] iron-sulphur domain 0.53 43.0 3.34e-01 95.7% 53.6%
3dghA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.52 35.0 2.72e-01 70.2% 28.5%
3i9v700 3.30.920.80 Alpha Beta › 2-Layer Sandwich › Metal Transport, Frataxin; Chain A › NADH-quinone oxidoreductase, subunit 15 0.52 42.0 3.26e-01 100.0% 42.5%
3bt7A02 2.40.50.1070 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.52 37.0 2.61e-01 76.6% 36.6%
2a3vA02 1.10.443.10 Mainly Alpha › Orthogonal Bundle › hpI Integrase; Chain A › Intergrase catalytic core 0.51 45.0 2.92e-01 100.0% 62.1%
1u2kA02 1.10.420.10 Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 2 › Peroxidase, domain 2 0.51 40.0 3.03e-01 93.6% 38.3%
5nr1A01 3.40.30.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaredoxin › Glutaredoxin 0.50 38.0 3.14e-01 93.6% 75.5%
2w9jA00 3.30.720.10 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › Signal recognition particle alu RNA binding heterodimer, srp9/1 0.50 39.0 3.61e-01 100.0% 70.4%
ECOD (66)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4106397 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.86 77.0 6.53e-01 100.0% 74.7%
3828070 252.1.1.0 a+b two layers › DNA-binding domain › Methyl-CpG-binding domain, MBD › Methyl-CpG-binding domain, MBD 0.81 63.0 6.00e-01 100.0% 72.7%
3678841 330.1.1.1 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.78 67.0 5.57e-01 100.0% 60.0%
3370322 330.1.1.1 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.78 68.0 5.50e-01 100.0% 58.9%
3221077 330.1.1.1 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.77 67.0 5.68e-01 100.0% 61.3%
3610595 3131.1.1.3 a+b two layers › FYR domain › FYR domain › FYR domain › FYRC 0.77 66.0 4.76e-01 100.0% 35.5%
3319893 330.1.1.1 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.77 65.0 5.18e-01 100.0% 69.0%
3426675 252.1.1.1 a+b two layers › DNA-binding domain › Methyl-CpG-binding domain, MBD › Methyl-CpG-binding domain, MBD › MBD 0.76 57.0 5.37e-01 100.0% 66.1%
3327575 330.1.1.1 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.76 67.0 5.24e-01 100.0% 49.0%
3299579 330.1.1.1 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.76 68.0 5.94e-01 100.0% 68.6%
3434453 252.1.1.0 a+b two layers › DNA-binding domain › Methyl-CpG-binding domain, MBD › Methyl-CpG-binding domain, MBD 0.75 55.0 5.85e-01 97.9% 100.0%
3436776 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.74 64.0 5.07e-01 100.0% 54.0%
4959885 4100.1.1.0 a+b duplicates or obligate multimers › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like › TTHA1013/TTHA0281-like 0.74 62.0 5.20e-01 100.0% 54.1%
1168794 330.1.1.8 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › Dicer_dsRBD 0.73 63.0 5.08e-01 100.0% 54.7%
4345436 4325.1.1.1 mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF1508 0.72 60.0 5.27e-01 100.0% 61.3%
3481288 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.72 63.0 4.78e-01 100.0% 49.6%
3597599 214.1.1.0 a+b two layers › SH2 › SH2 › SH2 0.72 60.0 4.80e-01 100.0% 46.0%
3700429 223.2.1.6 a+b three layers › Profilin-like › profilin-like › profilin-like › uDENN 0.71 61.0 4.42e-01 100.0% 34.3%
3940690 375.1.1.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.71 46.0 3.56e-01 72.3% 29.5%
3969097 4325.1.1.0 mixed a+b and a/b › YegP-like › YegP-like › YegP-like 0.71 60.0 5.94e-01 100.0% 90.0%
3346241 252.1.1.0 a+b two layers › DNA-binding domain › Methyl-CpG-binding domain, MBD › Methyl-CpG-binding domain, MBD 0.71 52.0 5.20e-01 100.0% 80.0%
3699899 214.1.1.6 a+b two layers › SH2 › SH2 › SH2 › SH2_2 0.71 57.0 4.41e-01 100.0% 38.3%
5018724 872.3.1.0 a+b two layers › Dodecin subunit-like › YbjQ-like › YbjQ-like 0.69 56.0 4.58e-01 100.0% 47.4%
4944389 375.1.1.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.69 44.0 4.02e-01 95.7% 47.7%
3606500 375.8.1.1 few secondary structure elements › Rubredoxin-like › Zinc-binding domain of translation initiation factor 2 beta › Zinc-binding domain of translation initiation factor 2 beta › eIF-5_eIF-2B 0.68 46.0 4.30e-01 72.3% 65.0%
4014180 708.1.2.0 beta complex topology › ETN0001 domain-like › ETN0001 domain-like › Mss4-like 0.67 49.0 3.68e-01 80.9% 31.7%
3586676 386.1.1.18 few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › zf-C2H2_jaz 0.65 47.0 4.85e-01 100.0% 97.5%
4004358 252.2.1.3 a+b two layers › DNA-binding domain › GCC-box binding domain-like › GCC-box binding domain-like › Arm-DNA-bind_1 0.65 52.0 5.19e-01 95.7% 92.0%
3461521 243.1.1.0 a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.65 43.0 3.29e-01 70.2% 33.9%
4123857 391.1.2.0 few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › VWC domain-related 0.65 40.0 4.27e-01 70.2% 72.5%
3726946 708.1.2.6 beta complex topology › ETN0001 domain-like › ETN0001 domain-like › Mss4-like › GFA 0.65 47.0 3.62e-01 80.9% 36.5%
4182599 223.2.1.20 a+b three layers › Profilin-like › profilin-like › profilin-like › Fuz_longin_1 0.64 53.0 3.84e-01 100.0% 32.3%
3408937 330.1.1.1 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like › dsrm 0.64 54.0 4.58e-01 100.0% 56.2%
3783916 375.1.1.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.64 47.0 4.52e-01 80.9% 74.5%
3499345 4325.1.1.0 mixed a+b and a/b › YegP-like › YegP-like › YegP-like 0.64 46.0 3.87e-01 78.7% 48.2%
3702281 375.8.1.0 few secondary structure elements › Rubredoxin-like › Zinc-binding domain of translation initiation factor 2 beta › Zinc-binding domain of translation initiation factor 2 beta 0.64 43.0 4.16e-01 70.2% 69.1%
3544243 277.1.1.1 a+b two layers › PX domain › PX domain › PX domain › PX 0.64 51.0 4.16e-01 100.0% 79.0%
3390566 330.1.1.0 a+b two layers › dsRBD-like › dsRNA-binding domain-like › dsRNA-binding domain-like 0.63 51.0 4.16e-01 100.0% 45.0%
3384331 2.1.1.0 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.63 50.0 4.18e-01 89.4% 56.5%
3722582 708.1.2.6 beta complex topology › ETN0001 domain-like › ETN0001 domain-like › Mss4-like › GFA 0.63 47.0 3.42e-01 83.0% 28.9%
4927858 375.1.1.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.63 41.0 3.93e-01 80.9% 56.4%
3689391 708.1.2.6 beta complex topology › ETN0001 domain-like › ETN0001 domain-like › Mss4-like › GFA 0.63 46.0 3.33e-01 80.9% 27.5%
4926953 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.63 51.0 3.86e-01 93.6% 37.7%
3201717 708.1.2.6 beta complex topology › ETN0001 domain-like › ETN0001 domain-like › Mss4-like › GFA 0.62 45.0 3.18e-01 80.9% 23.0%
3765005 109.4.1.0 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.62 47.0 2.61e-01 85.1% 8.6%
5005182 375.1.1.9 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related › zf-C4_Topoisom 0.62 53.0 4.36e-01 100.0% 52.2%
3237220 220.1.1.84 beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_15 0.62 45.0 3.47e-01 80.9% 59.1%
3181514 708.1.2.6 beta complex topology › ETN0001 domain-like › ETN0001 domain-like › Mss4-like › GFA 0.62 46.0 3.40e-01 83.0% 30.0%
3179640 708.1.2.6 beta complex topology › ETN0001 domain-like › ETN0001 domain-like › Mss4-like › GFA 0.61 46.0 3.33e-01 83.0% 27.9%
3282699 2.1.1.15 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › tRNA_anti-codon 0.61 50.0 3.86e-01 95.7% 62.6%
4528707 2.1.1.15 beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › tRNA_anti-codon 0.60 49.0 3.79e-01 93.6% 64.5%
3606532 2484.6.1.0 mixed a+b and a/b › Ribonuclease H-like › Periplasmic domain of ExbD/TolR › Periplasmic domain of ExbD/TolR 0.60 48.0 4.03e-01 100.0% 50.0%
3222570 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.60 44.0 3.45e-01 85.1% 37.4%
3907024 260.1.1.1 a+b duplicates or obligate multimers › beta-hairpin-alpha-hairpin repeat › beta-hairpin-alpha-hairpin repeat › beta-hairpin-alpha-hairpin repeat › Plectin 0.59 51.0 3.09e-01 97.9% 18.8%
4035868 2003.1.2.1 a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › Pyr_redox 0.59 39.0 2.97e-01 70.2% 27.7%
4094132 11.1.1.156 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › bMG3 0.58 45.0 3.71e-01 93.6% 74.0%
3605369 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.58 43.0 4.13e-01 80.9% 76.4%
3990293 4.8.1.0 beta barrels › SH3 › Chromo domain-like › Chromo domain-like 0.58 41.0 4.04e-01 80.9% 70.9%
3559703 101.1.8.12 alpha arrays › HTH › HTH › DNA breaking-rejoining enzymes › DUF3504 0.57 49.0 3.43e-01 100.0% 55.7%
4440689 325.1.7.0 a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.56 43.0 4.01e-01 89.4% 73.8%
3251163 245.1.1.1 a+b two layers › Ribonuclease PH domain 2-like › Ribonuclease PH domain 2 › Ribonuclease PH domain 2 › RNase_PH_C 0.56 49.0 4.00e-01 100.0% 84.4%
3742330 220.1.1.8 beta barrels › PH domain-like › PH domain-like › PH domain-like › GRAM 0.54 46.0 3.44e-01 100.0% 38.3%
4061485 4967.1.1.0 alpha bundles › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases › helical bundle domain in reverse transcriptase-like polymerases 0.54 41.0 2.82e-01 83.0% 49.7%
3971733 11.9.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › FAH › FAH 0.53 40.0 2.55e-01 91.5% 15.3%
3285829 4.1.1.425 beta barrels › SH3 › SH3 › SH3 › RNHCP 0.52 36.0 2.90e-01 72.3% 32.4%
4962459 220.1.1.0 beta barrels › PH domain-like › PH domain-like › PH domain-like 0.51 44.0 3.65e-01 100.0% 53.4%