Back to structures

NC_070912.1__YP_010664117.1__PQA64_gp17__00017

Bact-Vir

NC_070912.1__YP_010664117.1__PQA64_gp17__00017

Identity

Accession:
NC_070912 ↗
Kingdom:
phage

Quality

91.5 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 2-129
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF06891.18 best P2_Phage_GpR 140.5 5.00e-41 100.0% 96.2%
CATH (43)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2w4yA00 2.40.160.220 Mainly Beta › Beta Barrel › Porin › 0.75 34.0 3.53e-01 79.7% 45.1%
2rjzA02 3.30.70.60 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › Ribosomal protein S6/Translation elongation factor EF1B 0.71 50.0 5.57e-01 89.1% 92.9%
7k0xA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.70 35.0 4.40e-01 70.3% 78.2%
6x4tA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.69 37.0 4.46e-01 81.2% 78.8%
3n5fA02 3.30.70.360 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.65 44.0 4.60e-01 75.8% 76.3%
2y3uA02 3.30.980.50 Alpha Beta › 2-Layer Sandwich › Threonyl-tRNA Synthetase; Chain A, domain 2 › 0.64 48.0 5.08e-01 89.1% 87.6%
1h2iA01 3.30.390.80 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › DNA repair protein Rad52/59/22 0.64 41.0 3.88e-01 99.2% 54.7%
2bc4A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.64 38.0 4.07e-01 88.3% 67.0%
2gjvA00 3.30.2000.10 Alpha Beta › 2-Layer Sandwich › STM4215-like › Phage tail protein-like 0.64 54.0 5.37e-01 91.4% 97.1%
6toaF01 3.30.2000.30 Alpha Beta › 2-Layer Sandwich › STM4215-like › 0.64 53.0 5.27e-01 88.3% 97.7%
4ofyD02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.64 40.0 4.37e-01 89.8% 75.7%
3hz7A00 3.30.110.40 Alpha Beta › 2-Layer Sandwich › Translation Initiation Factor IF3 › TusA-like domain 0.62 32.0 4.09e-01 74.2% 86.3%
5aj3E01 3.30.230.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.62 33.0 4.06e-01 98.4% 80.2%
4ccvA00 3.10.450.10 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.62 39.0 4.07e-01 100.0% 68.7%
4acvA00 3.30.2000.30 Alpha Beta › 2-Layer Sandwich › STM4215-like › 0.62 51.0 5.28e-01 89.8% 95.0%
3njcA00 3.30.1380.20 Alpha Beta › 2-Layer Sandwich › Muramoyl-pentapeptide Carboxypeptidase; domain 2 › Trafficking protein particle complex subunit 3 0.61 42.0 3.95e-01 86.7% 58.2%
3u83A02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 37.0 4.12e-01 88.3% 77.2%
4r6uA03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 36.0 3.93e-01 88.3% 72.8%
6dw1A00 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.59 50.0 4.23e-01 90.6% 60.5%
4i0kA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 41.0 4.64e-01 87.5% 97.9%
3o4oB03 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 39.0 4.17e-01 89.1% 80.7%
4dmzA02 3.30.70.2880 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.57 38.0 3.80e-01 81.2% 63.5%
4bfiB02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.57 39.0 4.56e-01 80.5% 100.0%
1gkuB07 2.60.510.20 Mainly Beta › Sandwich › EV matrix protein fold › 0.56 32.0 3.51e-01 97.7% 67.6%
8eisA01 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.56 47.0 4.05e-01 90.6% 63.5%
2w8eA00 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.55 46.0 3.95e-01 89.8% 60.1%
2f86B00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.55 44.0 4.47e-01 100.0% 84.5%
4ndhB00 3.30.428.10 Alpha Beta › 2-Layer Sandwich › HIT family, subunit A › HIT-like 0.55 37.0 3.32e-01 84.4% 49.4%
1pu4A03 2.70.98.20 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Copper amine oxidase, catalytic domain 0.54 44.0 3.16e-01 89.1% 89.7%
4fomA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 39.0 4.44e-01 87.5% 97.0%
3igqC00 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.54 46.0 4.08e-01 92.2% 65.2%
6y1zA01 2.70.170.10 Mainly Beta › Distorted Sandwich › Acetylcholine Binding Protein; Chain: A, › Neurotransmitter-gated ion-channel ligand-binding domain 0.54 45.0 3.81e-01 90.6% 59.4%
4kghA00 3.15.10.10 Alpha Beta › Super Roll › Bactericidal permeability-increasing protein; domain 1 › Bactericidal permeability-increasing protein; domain 1 0.53 41.0 3.62e-01 100.0% 53.9%
4azsA02 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.53 33.0 3.91e-01 85.2% 96.3%
7ly5B01 3.40.109.10 Alpha Beta › 3-Layer(aba) Sandwich › NADH Oxidase › NADH Oxidase 0.53 42.0 3.97e-01 84.4% 97.4%
1y8oA02 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.52 43.0 3.92e-01 88.3% 91.2%
3cxjA00 3.30.1460.10 Alpha Beta › 2-Layer Sandwich › Yope Regulator; Chain: A, › 0.52 36.0 3.53e-01 78.9% 63.2%
3a76A01 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.52 43.0 4.22e-01 100.0% 80.6%
6secA03 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.52 42.0 3.25e-01 85.9% 95.4%
4ec6A00 3.10.450.540 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.52 35.0 3.73e-01 100.0% 79.8%
4bxiA00 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.52 41.0 3.97e-01 85.9% 85.6%
3ub1A01 3.10.450.540 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.51 40.0 3.92e-01 100.0% 76.5%
3a0rA03 3.30.565.10 Alpha Beta › 2-Layer Sandwich › Heat Shock Protein 90 › Histidine kinase-like ATPase, C-terminal domain 0.50 41.0 3.94e-01 87.5% 92.5%
ECOD (53)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3943477 310.3.1.9 a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related › P2_Phage_GpR 0.96 92.0 9.16e-01 100.0% 97.7%
4955075 310.3.1.0 a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related 0.72 41.0 5.38e-01 82.0% 100.0%
197096 310.3.1.1 a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related › PilO 0.72 52.0 5.12e-01 88.3% 70.4%
None 0.69 48.0 5.32e-01 88.3% 91.0%
3970985 304.124.1.9 a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › Phage_tail_terminator_9 0.68 56.0 5.51e-01 89.1% 98.6%
5040945 304.124.1.0 a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.68 62.0 5.86e-01 97.7% 95.3%
4562028 310.3.1.0 a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related 0.67 51.0 4.94e-01 89.1% 71.7%
4942841 243.1.1.0 a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.66 38.0 4.05e-01 100.0% 63.5%
3959285 243.1.1.0 a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.65 40.0 4.85e-01 100.0% 94.0%
3513177 243.3.1.0 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.65 41.0 4.52e-01 100.0% 77.1%
3964886 304.124.1.0 a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.65 52.0 5.11e-01 85.9% 97.1%
5454 304.124.1.2 a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like › Gp37 0.64 54.0 5.40e-01 91.4% 98.5%
3934522 243.3.1.0 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.64 38.0 4.33e-01 100.0% 78.9%
3729387 243.1.1.0 a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.63 43.0 4.60e-01 100.0% 80.9%
4939879 315.1.1.15 a+b two layers › Tautomerase/MIF-like › Tautomerase/MIF › Tautomerase/MIF › DUF5402 0.63 43.0 4.47e-01 85.2% 75.0%
5083619 304.124.1.0 a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.62 51.0 4.95e-01 88.3% 95.8%
3493155 5087.3.1.2 beta meanders › Lipovitellin-phosvitin complex › Lipovitellin LV-1C › Lipovitellin LV-1C › MTP_lip_bd 0.62 35.0 2.63e-01 100.0% 20.9%
4928893 304.124.1.0 a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.61 51.0 4.95e-01 89.8% 93.1%
5083880 304.124.1.0 a+b two layers › Alpha-beta plaits › Phage tail protein-like › Phage tail protein-like 0.61 51.0 4.90e-01 90.6% 94.5%
4957232 310.3.1.0 a+b two layers › RRF/tRNA synthetase additional domain-like › General secretion pathway protein M (EpsM) periplasmic domain-related › General secretion pathway protein M (EpsM) periplasmic domain-related 0.60 44.0 4.94e-01 87.5% 98.0%
3372143 881.1.1.1 a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like › PsbP 0.60 39.0 4.00e-01 100.0% 66.4%
4663230 225.1.1.0 a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase 0.59 42.0 4.07e-01 86.7% 65.5%
5034763 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.58 40.0 3.83e-01 87.5% 60.0%
3628642 5.1.4.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.58 32.0 2.36e-01 100.0% 18.1%
3957386 883.1.1.0 a+b complex topology › Aha1/BPI domain-like › Aha1/BPI domain-like › Aha1/BPI domain-like 0.58 41.0 3.62e-01 100.0% 50.6%
3198011 11.1.1.507 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › DUF3712 0.58 41.0 3.84e-01 88.3% 59.4%
5041901 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 40.0 3.91e-01 87.5% 65.0%
3950026 243.1.1.0 a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.57 45.0 4.45e-01 100.0% 78.4%
3504703 243.3.1.0 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.57 35.0 3.96e-01 100.0% 81.1%
3298052 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.57 38.0 4.06e-01 85.9% 78.2%
3384696 225.1.1.3 a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.56 49.0 4.45e-01 96.1% 89.6%
4948955 243.3.1.0 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.56 30.0 2.86e-01 100.0% 40.8%
3233697 11.12.1.1 beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.56 47.0 3.84e-01 89.8% 58.7%
3994685 11.12.1.1 beta sandwiches › Immunoglobulin-like beta-sandwich › Nicotinic receptor ligand binding domain-like › Nicotinic receptor ligand binding domain-like › Neur_chan_LBD 0.55 46.0 3.70e-01 89.8% 47.2%
3988939 225.1.1.17 a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c+His_kinase 0.55 46.0 4.17e-01 89.1% 85.1%
4975701 304.102.1.2 a+b two layers › Alpha-beta plaits › Pseudouridine synthase › Pseudouridine synthase › TruD 0.54 47.0 3.88e-01 94.5% 88.7%
3727965 4955.1.1.8 a+b two layers › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › permuted ferredoxin-like domain in yeast RNA-polymerase beta-prime subunit › AtuA_ferredoxin 0.53 43.0 3.45e-01 100.0% 43.5%
3613801 5.1.2.0 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed 0.53 36.0 2.66e-01 100.0% 24.1%
3282685 243.1.1.0 a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.53 42.0 4.35e-01 100.0% 89.2%
3957821 243.1.1.77 a+b two layers › Cystatin-like › NTF2-like › NTF2-like › PF29518 0.53 42.0 4.23e-01 100.0% 82.8%
3723425 206.1.1.1 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.53 41.0 3.06e-01 82.0% 47.1%
4335602 225.1.1.3 a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.52 42.0 4.14e-01 86.7% 95.0%
3476800 328.1.1.0 a+b two layers › IF3-like › AlbA-like › AlbA-like 0.52 38.0 3.93e-01 75.8% 92.5%
4944707 11.1.5.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f 0.51 45.0 4.42e-01 96.1% 97.1%
5007992 11.1.1.51 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › LEA_2 0.51 37.0 3.73e-01 89.8% 73.8%
5044753 11.1.5.59 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Common fold of diphtheria toxin/transcription factors/cytochrome f › DUF4139 0.51 45.0 4.50e-01 96.1% 96.2%
3373981 206.1.1.0 a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.51 38.0 3.17e-01 99.2% 45.0%
3285905 243.1.1.0 a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.50 39.0 3.93e-01 100.0% 80.8%
3829832 243.1.1.2 a+b two layers › Cystatin-like › NTF2-like › NTF2-like › NTF2 0.50 33.0 3.55e-01 88.3% 77.3%
3495520 11.1.1.0 beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.50 45.0 3.76e-01 100.0% 74.1%
4175473 5087.3.1.1 beta meanders › Lipovitellin-phosvitin complex › Lipovitellin LV-1C › Lipovitellin LV-1C › Vit_open_b-sht 0.50 34.0 2.52e-01 82.8% 27.2%
3823551 243.3.1.0 a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.50 40.0 3.85e-01 84.4% 95.2%
4593105 243.1.1.3 a+b two layers › Cystatin-like › NTF2-like › NTF2-like › Scytalone_dh 0.50 37.0 3.81e-01 100.0% 80.0%