←Back to structures

NC_056724.1__YP_010133253.1__K3164_gp33__00033

Bact-Vir

NC_056724.1__YP_010133253.1__K3164_gp33__00033

Identity

Accession:
NC_056724 ↗
Kingdom:
phage

Quality

83.2 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Sandinevirus› Lactococcus_phage_BK5-T

TaxID: 31754

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 high residues 31-166
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF18885.7 best DUF5648 128.2 3.60e-37 98.5% 97.8%
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2dleA01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.54 22.0 2.75e-01 83.8% 57.0%
ECOD (2)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3512155 560.1.1.3 ↗ few secondary structure elements › H-NS histone-like proteins, C-terminal domain › H-NS histone-like proteins, C-terminal domain › H-NS histone-like proteins, C-terminal domain › DUF5648 0.82 55.0 6.60e-01 99.3% 97.9%
3973988 5.1.2.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed 0.78 69.0 4.61e-01 100.0% 27.1%
D2 high residues 174-256
PDB
Domain cluster: representative
CATH (49)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3d4eA02 3.30.1450.10 Alpha Beta › 2-Layer Sandwich › Beta-lactamase Inhibitory Protein; Chain:B, domain 1 › 0.86 69.0 7.12e-01 100.0% 88.5%
3d4eA01 3.30.1450.10 Alpha Beta › 2-Layer Sandwich › Beta-lactamase Inhibitory Protein; Chain:B, domain 1 › 0.83 68.0 6.83e-01 100.0% 85.7%
1mmuA00 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.68 51.0 3.33e-01 78.3% 37.5%
3imhA00 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.67 50.0 3.30e-01 78.3% 37.7%
3mg1B02 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.67 49.0 4.29e-01 78.3% 88.0%
3bb9B00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.66 48.0 4.17e-01 75.9% 91.2%
5ig0A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.66 49.0 4.18e-01 78.3% 91.6%
3rgaA01 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.65 48.0 4.13e-01 78.3% 87.2%
4exrA02 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.65 43.0 4.62e-01 78.3% 78.9%
1wnhA02 3.10.450.10 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.65 48.0 4.23e-01 78.3% 65.0%
2kxgA00 3.10.450.10 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.63 47.0 4.49e-01 78.3% 77.9%
3djwA00 3.30.160.300 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.63 56.0 5.37e-01 98.8% 85.3%
3bcyA00 3.40.1000.40 Alpha Beta › 3-Layer(aba) Sandwich › Protein Transport Mog1p; Chain A › Respiratory growth induced protein 1 0.63 57.0 4.69e-01 100.0% 84.2%
1f49A05 2.70.98.10 Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › 0.63 47.0 3.20e-01 78.3% 40.0%
3eyrA00 3.15.10.40 Alpha Beta › Super Roll › Bactericidal permeability-increasing protein; domain 1 › Uncharacterised protein PF07273 family, DUF1439 0.63 44.0 3.49e-01 73.5% 49.1%
1olzA01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.62 46.0 2.84e-01 77.1% 34.3%
7bwcA01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.62 45.0 3.05e-01 78.3% 19.8%
4mp8A01 3.30.1780.10 Alpha Beta › 2-Layer Sandwich › ornithine cyclodeaminase, domain 1 › ornithine cyclodeaminase, domain 1 0.62 48.0 3.89e-01 84.3% 72.7%
2h36X00 3.30.160.300 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.62 56.0 5.13e-01 100.0% 77.8%
3qeeB00 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.62 43.0 2.96e-01 77.1% 20.4%
4ftxB01 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.61 46.0 3.98e-01 100.0% 51.6%
1s5aB00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.61 45.0 3.80e-01 78.3% 83.2%
2r4iA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.61 45.0 3.98e-01 78.3% 91.1%
1uuzB00 3.40.1420.10 Alpha Beta › 3-Layer(aba) Sandwich › Inhibitor of vertebrate lysozyme, Ivy › Inhibitor of vertebrate lysozyme 0.61 45.0 3.87e-01 78.3% 56.2%
1vqzA02 3.30.390.50 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › CO dehydrogenase flavoprotein, C-terminal domain 0.60 38.0 3.76e-01 74.7% 60.2%
3lh4A00 3.10.450.10 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.59 47.0 4.23e-01 86.7% 98.3%
3nvqA01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.59 43.0 2.73e-01 78.3% 17.7%
3ecrB03 3.30.160.40 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Porphobilinogen deaminase, C-terminal domain 0.58 43.0 4.03e-01 78.3% 82.4%
1ln1A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.57 46.0 3.59e-01 91.6% 68.0%
3ff2A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.57 45.0 4.09e-01 89.2% 72.6%
3t1oA00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.57 47.0 3.64e-01 92.8% 91.1%
2i99A01 3.30.1780.10 Alpha Beta › 2-Layer Sandwich › ornithine cyclodeaminase, domain 1 › ornithine cyclodeaminase, domain 1 0.57 47.0 3.91e-01 91.6% 74.0%
8aa0E01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.56 40.0 2.81e-01 77.1% 22.5%
2qm4A01 2.170.210.10 Mainly Beta › Beta Complex › Dna Repair Protein Xrcc4; Chain: A, domain 1 › DNA double-strand break repair and VJ recombination XRCC4, N-terminal 0.56 43.0 3.57e-01 81.9% 70.6%
3cwvA02 3.30.230.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.54 38.0 3.12e-01 73.5% 76.8%
4wrnA02 2.60.40.3210 Mainly Beta › Sandwich › Immunoglobulin-like › Zona pellucida, ZP-N domain 0.53 42.0 3.97e-01 86.7% 99.0%
3soyA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 47.0 3.96e-01 97.6% 80.3%
3pijA01 2.115.10.20 Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43 0.53 45.0 2.93e-01 92.8% 59.9%
3kspA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 48.0 4.09e-01 97.6% 79.8%
4h3uA00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 43.0 3.80e-01 92.8% 69.2%
1gpqB00 3.40.1420.10 Alpha Beta › 3-Layer(aba) Sandwich › Inhibitor of vertebrate lysozyme, Ivy › Inhibitor of vertebrate lysozyme 0.53 44.0 3.77e-01 97.6% 57.8%
1l3aA00 2.30.31.10 Mainly Beta › Roll › Transcriptional Co-activator pc4; Chain A › Transcriptional Coactivator Pc4; Chain A 0.53 40.0 3.25e-01 81.9% 80.7%
2w4yA00 2.40.160.220 Mainly Beta › Beta Barrel › Porin › 0.53 42.0 3.72e-01 86.7% 63.1%
7c5yA02 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.53 47.0 3.83e-01 98.8% 91.5%
4zwnB00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 36.0 2.53e-01 72.3% 36.0%
2bolA03 2.60.40.790 Mainly Beta › Sandwich › Immunoglobulin-like › 0.52 38.0 3.68e-01 77.1% 76.3%
3k44B00 3.30.2450.30 Alpha Beta › 2-Layer Sandwich › Secreted effector protein pipB2 fold › 0.51 46.0 3.88e-01 100.0% 80.0%
3dm8A00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.50 43.0 3.76e-01 100.0% 65.2%
3q31A00 3.10.200.10 Alpha Beta › Roll › Carbonic Anhydrase II › Alpha carbonic anhydrase 0.50 44.0 3.22e-01 98.8% 39.8%
ECOD (62)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1758198 809.1.1.3 ↗ a+b two layers › BLIP-like › beta-lactamase-inhibitor protein, BLIP › beta-lactamase-inhibitor protein, BLIP › DUF3862 0.86 69.0 7.16e-01 100.0% 89.6%
1760289 809.1.1.3 ↗ a+b two layers › BLIP-like › beta-lactamase-inhibitor protein, BLIP › beta-lactamase-inhibitor protein, BLIP › DUF3862 0.83 68.0 6.83e-01 100.0% 85.7%
4944962 331.1.1.0 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like 0.73 56.0 5.23e-01 90.4% 67.0%
4949536 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.72 46.0 2.94e-01 78.3% 14.8%
3575714 5.1.4.329 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › PF30693 0.70 52.0 3.24e-01 77.1% 18.3%
4017305 5.1.3.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed 0.70 51.0 3.43e-01 77.1% 21.7%
3183547 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.69 52.0 4.30e-01 78.3% 82.1%
4029652 5.1.4.16 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › CPSF_A 0.68 50.0 3.17e-01 77.1% 20.0%
3819476 5.1.4.430 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › PF30506 0.68 50.0 3.04e-01 77.1% 17.3%
3651019 5.1.4.101 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › DUF1618 0.66 49.0 3.36e-01 78.3% 27.6%
2073819 5.1.2.8 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed › Glyco_hydro_43 0.65 48.0 3.20e-01 77.1% 24.3%
3584167 220.1.1.123 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like › PH_SSH1-like_1st 0.65 48.0 4.15e-01 78.3% 57.7%
3935161 243.3.1.0 ↗ a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin 0.65 48.0 4.48e-01 78.3% 77.1%
3694785 4099.1.1.10 ↗ a+b two layers › Kinetochore globular domain-like › Kinetochore globular domain-like › Kinetochore globular domain-like › Med1 0.65 47.0 3.45e-01 75.9% 29.8%
3255320 4096.1.1.1 ↗ a+b two layers › NAP-like › NAP-like › NAP-like › NAP 0.64 44.0 3.40e-01 72.3% 38.9%
4933284 3692.1.1.1 ↗ a+b two layers › Ornithine cyclodeaminase-like enzymes dimerization domain › Ornithine cyclodeaminase-like enzymes dimerization domain › Ornithine cyclodeaminase-like enzymes dimerization domain › OCD_Mu_crystall 0.63 49.0 4.06e-01 83.1% 77.1%
3169468 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.62 45.0 2.91e-01 77.1% 19.3%
3583345 5.1.4.288 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › APEH_N 0.62 46.0 2.90e-01 98.8% 14.8%
3352484 145.1.1.0 ↗ alpha arrays › F-box domain › F-box domain › F-box domain 0.62 45.0 2.91e-01 77.1% 16.8%
3056279 4051.1.1.2 ↗ a+b two layers › a+b domain in Capz › a+b domain in Capz › a+b domain in Capz › F-actin_cap_A 0.62 46.0 3.63e-01 77.1% 42.9%
3681461 5.1.3.6 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Kelch_1 0.62 46.0 2.98e-01 78.3% 19.3%
4080312 4312.1.1.17 ↗ a+b two layers › RelE-like › RelE-like › RelE-like › DUF1609 0.61 51.0 4.18e-01 91.6% 74.2%
3359021 5.1.5.86 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › Kelch_1 0.61 45.0 2.98e-01 78.3% 19.5%
4134185 3692.1.1.1 ↗ a+b two layers › Ornithine cyclodeaminase-like enzymes dimerization domain › Ornithine cyclodeaminase-like enzymes dimerization domain › Ornithine cyclodeaminase-like enzymes dimerization domain › OCD_Mu_crystall 0.61 52.0 4.33e-01 91.6% 79.9%
4511768 5.1.3.117 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Kelch_1+Kelch_KLHDC2_KLHL20_DRC7 0.61 50.0 3.28e-01 86.7% 82.2%
3990957 216.1.1.4 ↗ a+b two layers › UBC-like › UBC-like › UBC-like › RWD 0.61 45.0 3.81e-01 78.3% 54.8%
3538024 5.1.3.6 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Kelch_1 0.60 49.0 3.24e-01 86.7% 82.5%
3453043 5.1.3.65 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › DUF295 0.60 44.0 2.94e-01 77.1% 34.9%
3703427 708.1.1.0 ↗ beta complex topology › ETN0001 domain-like › ETN0001 domain-like › NAC/WRKY/GCM/WOPR domain 0.60 52.0 4.68e-01 98.8% 71.7%
5010078 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.60 49.0 3.13e-01 88.0% 83.2%
3826602 243.1.1.25 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › SnoaL_3 0.59 43.0 3.69e-01 78.3% 82.9%
3278459 881.1.1.33 ↗ a+b three layers › Mog1p/PsbP-like › Mog1p/PsbP-like › Mog1p/PsbP-like › PF26056 0.59 51.0 4.08e-01 100.0% 66.5%
3571633 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.58 40.0 2.46e-01 71.1% 24.8%
4196590 5.1.2.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed › Glyco_hydro_32N 0.58 50.0 3.32e-01 95.2% 44.3%
5055280 331.4.1.0 ↗ a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 0.58 48.0 4.02e-01 91.6% 60.0%
3215886 220.1.1.0 ↗ beta barrels › PH domain-like › PH domain-like › PH domain-like 0.58 44.0 3.65e-01 81.9% 80.0%
4641533 3692.1.1.1 ↗ a+b two layers › Ornithine cyclodeaminase-like enzymes dimerization domain › Ornithine cyclodeaminase-like enzymes dimerization domain › Ornithine cyclodeaminase-like enzymes dimerization domain › OCD_Mu_crystall 0.58 49.0 4.25e-01 91.6% 84.0%
None — 0.58 40.0 2.86e-01 85.5% 25.1%
4962576 3692.1.1.1 ↗ a+b two layers › Ornithine cyclodeaminase-like enzymes dimerization domain › Ornithine cyclodeaminase-like enzymes dimerization domain › Ornithine cyclodeaminase-like enzymes dimerization domain › OCD_Mu_crystall 0.58 47.0 3.95e-01 90.4% 73.1%
3424963 331.4.1.0 ↗ a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 0.57 50.0 4.12e-01 98.8% 80.6%
1283151 3692.1.1.1 ↗ a+b two layers › Ornithine cyclodeaminase-like enzymes dimerization domain › Ornithine cyclodeaminase-like enzymes dimerization domain › Ornithine cyclodeaminase-like enzymes dimerization domain › OCD_Mu_crystall 0.57 48.0 4.28e-01 91.6% 94.0%
3460207 5.1.3.67 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › FBA_1 0.57 41.0 2.93e-01 77.1% 23.7%
3973988 5.1.2.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed 0.57 41.0 2.58e-01 77.1% 14.8%
None — 0.56 50.0 4.43e-01 98.8% 85.8%
119272 3152.1.1.1 ↗ a+b two layers › Hypothetical Protein Vc0508 › Hypothetical Protein Vc0508 › Hypothetical Protein Vc0508 › DUF2787 0.56 44.0 3.69e-01 84.3% 52.4%
2722108 243.1.1.67 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › Cds6_C 0.56 49.0 4.27e-01 96.4% 81.5%
6390 243.1.1.25 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › SnoaL_3 0.56 50.0 4.39e-01 97.6% 87.4%
3706549 219.1.1.0 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases 0.56 48.0 3.25e-01 95.2% 63.1%
3724634 243.1.1.63 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › DUF6841 0.55 49.0 4.11e-01 97.6% 79.3%
3639154 331.4.1.27 ↗ a+b two layers › TBP-like › Kinase associated domain 1, KA1 › Kinase associated domain 1, KA1 › VASt 0.55 46.0 3.47e-01 91.6% 49.8%
3315222 243.1.1.89 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › DUF7074 0.55 39.0 3.74e-01 75.9% 72.0%
4420721 5.1.2.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed › Glyco_hydro_32N 0.55 48.0 3.15e-01 95.2% 43.5%
3961157 243.1.1.18 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like › SnoaL_2 0.55 46.0 4.16e-01 97.6% 70.0%
3960415 243.1.1.0 ↗ a+b two layers › Cystatin-like › NTF2-like › NTF2-like 0.54 45.0 4.00e-01 91.6% 74.2%
3593462 5.1.2.1 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 5-bladed › Glyco_hydro_32N 0.53 45.0 3.01e-01 100.0% 22.9%
5043415 9.1.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins 0.53 45.0 4.04e-01 96.4% 75.8%
3998680 206.1.1.0 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase 0.52 39.0 2.27e-01 80.7% 46.8%
3950370 881.4.1.3 ↗ a+b three layers › Mog1p/PsbP-like › C-terminal domain in sigma-E factor regulatory protein rseB › C-terminal domain in sigma-E factor regulatory protein rseB › DUF4245 0.52 42.0 3.58e-01 95.2% 68.4%
3486847 4.1.1.284 ↗ beta barrels › SH3 › SH3 › SH3 › SBNO 0.52 38.0 3.60e-01 80.7% 66.7%
None — 0.51 44.0 3.04e-01 97.6% 39.0%
2985481 3800.1.1.1 ↗ a+b two layers › Virion infectivity factor Vif › Virion infectivity factor Vif › Virion infectivity factor Vif › Vif 0.51 44.0 3.45e-01 94.0% 95.5%
3712376 2.1.1.225 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › PF30388 0.51 37.0 3.30e-01 77.1% 75.8%