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NC_021798.1__YP_008241602.1__Phi17-2_gp107__00107

Bact-Vir

NC_021798.1__YP_008241602.1__Phi17-2_gp107__00107

Identity

Accession:
NC_021798 ↗
Kingdom:
phage

Quality

78.4 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 1-79
PDB
Domain cluster: representative
CATH (19)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3thxB04 1.10.1420.10 Mainly Alpha › Orthogonal Bundle › MutS, DNA mismatch repair protein; Chain A, domain 3 › 0.69 56.0 4.74e-01 100.0% 53.9%
5yk4A04 1.10.1420.10 Mainly Alpha › Orthogonal Bundle › MutS, DNA mismatch repair protein; Chain A, domain 3 › 0.64 50.0 4.27e-01 100.0% 50.7%
1ewqA04 1.10.1420.10 Mainly Alpha › Orthogonal Bundle › MutS, DNA mismatch repair protein; Chain A, domain 3 › 0.61 47.0 4.06e-01 100.0% 50.7%
3onqA02 3.30.70.2730 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.58 39.0 3.94e-01 97.5% 67.9%
1q5yC00 3.30.70.1150 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT-like. Chain A, domain 2 0.57 38.0 3.76e-01 100.0% 65.9%
2ca9A02 3.30.70.1150 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT-like. Chain A, domain 2 0.57 38.0 3.65e-01 100.0% 60.7%
5cemA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.54 40.0 4.12e-01 92.4% 84.9%
7qprA02 3.30.460.10 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › Beta Polymerase, domain 2 0.54 45.0 3.93e-01 98.7% 80.0%
5mmjd02 3.10.290.10 Alpha Beta › Roll › Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A › RNA-binding S4 domain 0.54 44.0 4.16e-01 92.4% 91.8%
3bn0A00 3.30.1320.10 Alpha Beta › 2-Layer Sandwich › S16 Ribosomal Protein; Chain: A; › Ribosomal protein S16 0.53 35.0 3.31e-01 78.5% 54.7%
2gqqA02 3.30.70.920 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Lrp/AsnC effector binding domain/regulation of amino acid metabolism (RAM) domain 0.53 37.0 3.64e-01 100.0% 67.1%
2xzn800 3.30.63.20 Alpha Beta › 2-Layer Sandwich › Guanylate Kinase phosphate binding domain › 0.52 37.0 3.54e-01 84.8% 63.4%
5gt8D02 3.30.2130.10 Alpha Beta › 2-Layer Sandwich › VC0802-like › VC0802-like 0.52 38.0 3.37e-01 79.7% 81.1%
4g3cA01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.52 36.0 3.13e-01 73.4% 50.8%
3vgpA00 3.40.50.12610 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.51 44.0 3.52e-01 97.5% 84.7%
4xvoA01 2.60.40.3710 Mainly Beta › Sandwich › Immunoglobulin-like › 0.51 33.0 3.22e-01 100.0% 58.4%
1nrwA02 3.30.1240.10 Alpha Beta › 2-Layer Sandwich › Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 › 0.51 40.0 3.45e-01 87.3% 100.0%
3bv8A00 3.30.70.250 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Malonyl-CoA ACP transacylase, ACP-binding 0.51 31.0 3.11e-01 74.7% 56.5%
5erdB05 2.60.40.60 Mainly Beta › Sandwich › Immunoglobulin-like › Cadherins 0.50 36.0 3.41e-01 74.7% 62.8%
ECOD (27)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5053627 601.23.1.1 alpha bundles › Four-helical up-and-down bundle › DNA repair protein MutS, domain III › DNA repair protein MutS, domain III › MutS_III 0.62 51.0 3.50e-01 100.0% 24.3%
4076057 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 0.62 49.0 3.33e-01 100.0% 22.3%
4627664 601.23.1.1 alpha bundles › Four-helical up-and-down bundle › DNA repair protein MutS, domain III › DNA repair protein MutS, domain III › MutS_III 0.61 54.0 3.59e-01 100.0% 24.9%
4421536 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 0.60 49.0 3.33e-01 100.0% 23.5%
3203597 101.1.2.73 alpha arrays › HTH › HTH › winged helix domain › RNA_pol_Rpc82 0.59 50.0 4.38e-01 100.0% 96.2%
5009157 242.1.1.0 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.57 44.0 3.98e-01 83.5% 77.3%
4998391 242.1.1.0 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.56 43.0 4.13e-01 82.3% 80.0%
4993850 242.1.1.0 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.56 43.0 4.06e-01 82.3% 77.9%
4232356 101.1.2.517 alpha arrays › HTH › HTH › winged helix domain › RNA_pol_Rpc82, HTH_9, POLR3C_WHD 0.56 48.0 2.98e-01 100.0% 17.4%
3939951 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.56 41.0 4.09e-01 78.5% 83.7%
4223798 304.8.1.4 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › NikR_C 0.56 37.0 3.63e-01 100.0% 61.1%
3686958 304.9.1.43 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD › NCBP3 0.55 43.0 3.90e-01 87.3% 77.4%
3472013 601.23.1.1 alpha bundles › Four-helical up-and-down bundle › DNA repair protein MutS, domain III › DNA repair protein MutS, domain III › MutS_III 0.55 44.0 3.00e-01 100.0% 22.2%
172962 242.1.1.5 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › WhiA_N 0.55 41.0 3.82e-01 82.3% 63.2%
4668974 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.54 45.0 4.02e-01 97.5% 90.0%
4461165 101.1.2.773 alpha arrays › HTH › HTH › winged helix domain › YaaC 0.53 36.0 3.51e-01 75.9% 64.7%
5053351 101.1.2.0 alpha arrays › HTH › HTH › winged helix domain 0.52 39.0 3.74e-01 82.3% 70.5%
5035456 304.19.1.1 a+b two layers › Alpha-beta plaits › eIF-2-alpha, C-terminal domain › eIF-2-alpha, C-terminal domain › EIF_2_alpha 0.52 36.0 3.63e-01 100.0% 71.2%
5025961 304.8.1.0 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.52 31.0 3.29e-01 100.0% 67.1%
3669756 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.51 39.0 3.81e-01 82.3% 76.5%
3433011 304.9.1.0 a+b two layers › Alpha-beta plaits › RNA-binding domain, RBD › RNA-binding domain, RBD 0.51 39.0 3.42e-01 82.3% 58.3%
3997731 304.24.1.0 a+b two layers › Alpha-beta plaits › EF-G C-terminal domain-like › EF-G C-terminal domain-like 0.51 35.0 3.54e-01 100.0% 70.0%
4992659 242.1.1.0 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases 0.51 38.0 3.43e-01 82.3% 56.5%
3175120 242.1.1.2 a+b two layers › Homing endonucleases-like › Homing endonucleases › Homing endonucleases › LAGLIDADG_2 0.51 41.0 3.72e-01 91.1% 84.5%
3655963 304.8.1.0 a+b two layers › Alpha-beta plaits › ACT-like › ACT-like 0.50 35.0 3.64e-01 97.5% 82.9%
3295884 101.1.2.132 alpha arrays › HTH › HTH › winged helix domain › DUF3591 0.50 37.0 3.68e-01 81.0% 76.5%
4940154 3352.1.1.1 alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3 0.50 41.0 2.59e-01 96.2% 56.4%
D2 high residues 84-136
PDB
Domain cluster: representative
CATH (38)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3tfmA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.68 49.0 3.94e-01 75.5% 81.8%
1eazA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.66 47.0 3.79e-01 75.5% 76.7%
7ctpA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.66 46.0 3.55e-01 73.6% 81.7%
2piaA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.63 54.0 4.41e-01 100.0% 92.3%
2d9vA01 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.63 45.0 3.55e-01 75.5% 81.5%
3mfiA04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.62 50.0 4.02e-01 98.1% 95.0%
8h68A01 2.60.120.590 Mainly Beta › Sandwich › Jelly Rolls › Alpha-ketoglutarate-dependent dioxygenase AlkB-like 0.59 49.0 3.35e-01 98.1% 27.3%
8gz3B01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.58 48.0 4.11e-01 96.2% 100.0%
2xk0A00 2.30.30.140 Mainly Beta › Roll › SH3 type barrels. › 0.58 46.0 4.29e-01 90.6% 88.4%
3fgtA01 2.10.70.60 Mainly Beta › Ribbon › Complement Module; domain 1 › Phospholipase B-like, domain 1 0.58 32.0 3.22e-01 71.7% 49.1%
1ltlA03 2.20.28.10 Mainly Beta › Single Sheet › Rubrerythrin, domain 2 › 0.58 40.0 4.12e-01 73.6% 93.9%
2qh5B00 3.90.550.10 Alpha Beta › Alpha-Beta Complex › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A › Spore Coat Polysaccharide Biosynthesis Protein SpsA; Chain A 0.58 46.0 3.11e-01 100.0% 25.4%
2i1sA00 3.10.290.30 Alpha Beta › Roll › Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A › MM3350-like 0.57 44.0 3.11e-01 86.8% 50.0%
4u7cB04 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.57 47.0 3.87e-01 100.0% 95.4%
3nutB02 3.30.950.10 Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Tetrapyrrole methylase, C-terminal domain 0.56 45.0 3.61e-01 100.0% 86.7%
1ep3B01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.56 46.0 3.90e-01 100.0% 96.0%
1unnC00 3.30.1490.100 Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 › DNA polymerase, Y-family, little finger domain 0.56 45.0 3.72e-01 98.1% 86.5%
2d7eA01 3.40.1440.60 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › PriA, 3(prime) DNA-binding domain 0.56 43.0 3.76e-01 90.6% 54.4%
2i9dA00 3.30.559.10 Alpha Beta › 2-Layer Sandwich › Chloramphenicol Acetyltransferase › Chloramphenicol acetyltransferase-like domain 0.56 42.0 2.96e-01 90.6% 57.3%
7ylrA01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.56 44.0 3.67e-01 94.3% 100.0%
1yudA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.56 45.0 3.39e-01 98.1% 36.8%
3loiA01 2.60.120.10 Mainly Beta › Sandwich › Jelly Rolls › Jelly Rolls 0.55 45.0 3.36e-01 98.1% 36.3%
2vfrA02 3.30.465.10 Alpha Beta › 2-Layer Sandwich › Uridine Diphospho-n-acetylenolpyruvylglucosamine Reductase; domain 3 › 0.55 45.0 3.57e-01 100.0% 80.8%
2fjlA00 2.30.29.30 Mainly Beta › Roll › PH-domain like › Pleckstrin-homology domain (PH domain)/Phosphotyrosine-binding domain (PTB) 0.55 39.0 2.86e-01 75.5% 86.0%
2wyrB02 2.40.30.40 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Peptidase M42, domain 2 0.55 45.0 3.98e-01 98.1% 98.8%
1ln0A00 3.40.1440.10 Alpha Beta › 3-Layer(aba) Sandwich › GIY-YIG endonuclease › GIY-YIG endonuclease 0.54 37.0 3.19e-01 73.6% 65.2%
1xe0C00 2.60.120.340 Mainly Beta › Sandwich › Jelly Rolls › Nucleoplasmin core domain 0.54 44.0 3.73e-01 100.0% 71.3%
3gldA02 2.60.40.1140 Mainly Beta › Sandwich › Immunoglobulin-like › Collagen-binding surface protein Cna, B-type domain 0.54 43.0 3.36e-01 98.1% 52.2%
2dpyA00 3.40.50.12240 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.53 43.0 2.68e-01 100.0% 16.8%
3zoqC00 6.20.250.30 Special › Other non-globular › Double Stranded RNA Binding Domain › 0.53 36.0 3.64e-01 73.6% 88.7%
5mj6A03 2.60.40.1910 Mainly Beta › Sandwich › Immunoglobulin-like › 0.53 42.0 3.78e-01 94.3% 78.8%
3ndcA02 3.30.950.10 Alpha Beta › 2-Layer Sandwich › Methyltransferase, Cobalt-precorrin-4 Transmethylase; Domain 2 › Tetrapyrrole methylase, C-terminal domain 0.53 41.0 3.39e-01 100.0% 91.9%
1npsA00 2.60.20.10 Mainly Beta › Sandwich › Gamma-B Crystallin; domain 1 › Crystallins 0.51 41.0 3.68e-01 100.0% 71.6%
3h41A02 2.30.30.40 Mainly Beta › Roll › SH3 type barrels. › SH3 Domains 0.51 37.0 3.57e-01 86.8% 83.8%
4el6A00 2.60.20.10 Mainly Beta › Sandwich › Gamma-B Crystallin; domain 1 › Crystallins 0.51 39.0 3.49e-01 100.0% 63.9%
1bikA00 4.10.410.10 Few Secondary Structures › Irregular › Factor Xa Inhibitor › Pancreatic trypsin inhibitor Kunitz domain 0.51 39.0 3.20e-01 88.7% 69.1%
3ijfX00 3.40.140.10 Alpha Beta › 3-Layer(aba) Sandwich › Cytidine Deaminase; domain 2 › Cytidine Deaminase, domain 2 0.50 41.0 3.26e-01 98.1% 83.7%
5yv7A00 4.10.410.10 Few Secondary Structures › Irregular › Factor Xa Inhibitor › Pancreatic trypsin inhibitor Kunitz domain 0.50 37.0 3.61e-01 92.5% 71.7%
ECOD (30)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3720410 220.1.1.57 beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_20 0.67 47.0 3.52e-01 75.5% 63.7%
4928238 375.1.1.0 few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.64 40.0 4.10e-01 71.7% 64.2%
3603684 275.1.1.1 a+b two layers › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › MoeA-I/Ornithine decarboxylase-C/Reverse ferredoxin-like domain in RNA-polymerase › RNA_pol_Rpb1_2 0.64 54.0 5.03e-01 100.0% 98.6%
3611195 1.1.7.7 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 0.62 54.0 4.29e-01 100.0% 88.2%
5078886 331.3.1.0 a+b two layers › TBP-like › Bet v1-like › Bet v1-like 0.62 46.0 3.75e-01 84.9% 55.5%
3935630 3346.1.1.0 a+b two layers › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 › N-terminal domain in ubiquitin-fold modifier 1 specific protease UfSP2 0.61 41.0 2.83e-01 71.7% 26.8%
3558188 4.1.1.101 beta barrels › SH3 › SH3 › SH3 › Tudor_2 0.60 46.0 4.16e-01 83.0% 72.0%
3184038 72.1.1.0 beta sandwiches › gamma-Crystallin-like › gamma-Crystallin-like › gamma-Crystallin-like 0.59 49.0 4.37e-01 100.0% 66.3%
3958897 4187.2.1.0 a+b two layers › NosL/MerB-like › DUF2233 › DUF2233 0.58 47.0 3.76e-01 96.2% 50.0%
4345353 322.1.1.2 a+b two layers › HPr-like › HPr-like › HPr-like › 3H 0.57 45.0 3.71e-01 100.0% 67.5%
3924843 10.2.1.0 beta sandwiches › jelly-roll › Nucleoplasmin-like/VP (viral coat and capsid proteins) › Nucleoplasmin-like/VP (viral coat and capsid proteins) 0.57 47.0 3.25e-01 100.0% 41.0%
3672250 207.1.1.116 beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_FBXL15 0.56 46.0 3.28e-01 100.0% 42.6%
4942277 4261.1.1.0 a+b two layers › TrkA C-terminal domain-like › TrkA C-terminal domain-like › TrkA C-terminal domain-like 0.56 47.0 4.27e-01 100.0% 76.0%
4942475 4261.1.1.0 a+b two layers › TrkA C-terminal domain-like › TrkA C-terminal domain-like › TrkA C-terminal domain-like 0.56 46.0 4.24e-01 100.0% 76.0%
3388082 221.1.4.0 a+b two layers › beta-Grasp › Ubiquitin-related › Nqo1 middle domain-like 0.56 44.0 4.10e-01 96.2% 94.7%
5017741 221.6.1.1 a+b two layers › beta-Grasp › MM3350-like › MM3350-like › PRiA4_ORF3 0.55 44.0 3.16e-01 88.7% 58.9%
4969234 221.6.1.1 a+b two layers › beta-Grasp › MM3350-like › MM3350-like › PRiA4_ORF3 0.55 38.0 2.71e-01 73.6% 57.4%
3694265 1.1.7.7 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C › FAD_binding_6 0.55 43.0 3.49e-01 100.0% 81.5%
3775701 72.1.1.1 beta sandwiches › gamma-Crystallin-like › gamma-Crystallin-like › gamma-Crystallin-like › Crystall 0.55 44.0 3.97e-01 98.1% 67.1%
3597115 11.10.1.5 beta sandwiches › Immunoglobulin-like beta-sandwich › TRAF domain-like › TRAF domain-like › MATH_2 0.55 45.0 3.66e-01 100.0% 95.7%
4940416 11.1.4.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like 0.54 43.0 3.87e-01 94.3% 83.7%
3799510 384.1.1.1 few secondary structure elements › BPTI-like › BPTI-like › BPTI-like › Kunitz_BPTI 0.53 41.0 3.63e-01 88.7% 80.5%
3496352 1.1.7.0 beta barrels › cradle loop barrel › RIFT-related › Alanine racemase-C 0.53 41.0 3.41e-01 98.1% 90.8%
3599827 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.52 43.0 3.20e-01 100.0% 79.9%
3501768 382.1.1.0 few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.51 35.0 3.28e-01 73.6% 87.1%
4383356 3615.1.1.49 alpha bundles › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain › Bacterial dynamin-like protein helical domain › Dynamin_N 0.51 41.0 2.40e-01 100.0% 14.0%
3214786 384.1.1.0 few secondary structure elements › BPTI-like › BPTI-like › BPTI-like 0.51 34.0 3.23e-01 73.6% 54.3%
3618173 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.51 41.0 3.29e-01 100.0% 86.2%
3483611 221.1.1.0 a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like 0.50 40.0 3.54e-01 100.0% 75.6%
3584192 11.1.4.76 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like › NOMO_5th 0.50 37.0 3.34e-01 86.8% 60.0%