←Back to structures

MT735630.2__QWS69856.1__X__00031

Bact-Vir

MT735630.2__QWS69856.1__X__00031

Identity

Accession:
MT735630 ↗
Kingdom:
phage

Quality

77.0 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Vibrio_phage_vB_VpS_PG28

TaxID: 2759212

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 533-605
PDB
Domain cluster: representative
CATH (25)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4ks9A01 1.20.140.90 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Malonyl-CoA decarboxylase, oligemerization domain 0.78 71.0 5.84e-01 100.0% 96.0%
4nqwB00 1.10.10.1320 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Anti-sigma factor, zinc-finger domain 0.71 47.0 4.73e-01 74.0% 67.1%
2pbiA02 1.10.1240.60 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › 0.71 50.0 4.48e-01 74.0% 53.5%
3tmmA01 1.10.30.10 Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › High mobility group box domain 0.64 45.0 3.99e-01 75.3% 90.8%
2qtlA03 3.40.50.80 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Nucleotide-binding domain of ferredoxin-NADP reductase (FNR) module 0.63 52.0 4.08e-01 97.3% 42.6%
2ijqA00 1.10.3450.10 Mainly Alpha › Orthogonal Bundle › Hyaluronidase domain-like › TTHA0068-like 0.62 56.0 4.46e-01 100.0% 69.0%
1hssA00 1.10.110.10 Mainly Alpha › Orthogonal Bundle › Hydrophobic Seed Protein › Plant lipid-transfer and hydrophobic proteins 0.60 46.0 4.04e-01 83.6% 88.3%
5fcxA00 1.10.2090.10 Mainly Alpha › Orthogonal Bundle › orange carotenoid protein, domain 2 › Orange carotenoid-binding protein, N-terminal domain 0.59 50.0 3.99e-01 90.4% 48.2%
1k87A02 1.10.2060.10 Mainly Alpha › Orthogonal Bundle › PutA proline dehydrogenase (PRODH), domain 2 › PutA proline dehydrogenase (PRODH), domain 2 0.59 41.0 3.70e-01 75.3% 91.7%
3cf6E03 1.20.870.10 Mainly Alpha › Up-down Bundle › Son of sevenless (SoS) protein; Chain S, domain 1 › Son of sevenless (SoS) protein Chain: S domain 1 0.59 50.0 4.21e-01 98.6% 96.9%
4hbdA00 1.25.40.20 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Ankyrin repeat-containing domain 0.58 48.0 3.39e-01 93.2% 42.9%
1vw4L02 1.10.246.170 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › 0.58 47.0 4.58e-01 94.5% 83.5%
2c5uA02 1.10.3550.20 Mainly Alpha › Orthogonal Bundle › eoxyguanosinetriphosphate triphosphohydrolase fold › 0.57 36.0 3.03e-01 72.6% 35.9%
2jqtA00 1.20.1280.40 Mainly Alpha › Up-down Bundle › Monooxygenase › HHA 0.55 35.0 3.83e-01 72.6% 82.5%
1wgfA01 1.10.30.10 Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › High mobility group box domain 0.55 36.0 4.14e-01 79.5% 92.5%
3mg2B01 1.10.2090.10 Mainly Alpha › Orthogonal Bundle › orange carotenoid protein, domain 2 › Orange carotenoid-binding protein, N-terminal domain 0.54 48.0 3.83e-01 98.6% 49.7%
5cl3A00 1.25.10.90 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › 0.54 46.0 3.33e-01 98.6% 66.7%
7r97A01 1.10.1520.10 Mainly Alpha › Orthogonal Bundle › Ribonuclease iii, N-terminal Endonuclease Domain; Chain A › Ribonuclease III domain 0.54 41.0 3.29e-01 83.6% 78.4%
4edgA03 1.20.50.20 Mainly Alpha › Up-down Bundle › Pheromone ER-1 › DnaG, RNA polymerase domain, helical bundle 0.53 38.0 4.00e-01 91.8% 95.0%
3tjmA02 1.10.1470.20 Mainly Alpha › Orthogonal Bundle › Protein Yjbj; Chain: A; › Fatty acid synthase; domain 2 0.53 41.0 3.85e-01 89.0% 68.9%
3kmuA02 1.10.510.10 Mainly Alpha › Orthogonal Bundle › Transferase(Phosphotransferase); domain 1 › Transferase(Phosphotransferase) domain 1 0.53 44.0 3.40e-01 95.9% 79.9%
6jrpA01 1.10.30.10 Mainly Alpha › Orthogonal Bundle › DNA Binding (I), subunit A › High mobility group box domain 0.52 36.0 3.92e-01 78.1% 88.5%
4r9iA01 3.30.497.10 Alpha Beta › 2-Layer Sandwich › Antithrombin; Chain I, domain 2 › Antithrombin, subunit I, domain 2 0.51 43.0 3.00e-01 100.0% 78.1%
3l9tA01 1.10.1240.70 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › 0.50 42.0 4.09e-01 94.5% 100.0%
6cxtB01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.50 43.0 3.78e-01 97.3% 91.1%
ECOD (31)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3919069 176.1.1.2 ↗ alpha arrays › Annexin › Annexin › Annexin › Annexin_2 0.71 58.0 5.11e-01 97.3% 61.0%
3262856 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.71 56.0 3.18e-01 93.2% 8.1%
3561044 176.1.1.2 ↗ alpha arrays › Annexin › Annexin › Annexin › Annexin_2 0.71 58.0 5.36e-01 97.3% 71.1%
3723142 601.33.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › CHAD domain › CHAD domain 0.65 57.0 5.26e-01 97.3% 77.9%
3219629 109.4.1.2417 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Importin_rep_6, TPR_IPO5 0.64 55.0 3.31e-01 93.2% 22.8%
4956156 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.61 46.0 4.03e-01 91.8% 53.6%
3616859 532.2.1.0 ↗ alpha arrays › Type III secretion system domain-like › Type III secretion system domains › Type III secretion system domains 0.60 46.0 4.63e-01 93.2% 81.3%
1551399 4982.2.1.1 ↗ alpha arrays › KaiA/RbsU domain-like › Mitochondrial 54S ribosomal protein L8 C-terminal domain › Mitochondrial 54S ribosomal protein L8 C-terminal domain › Mrpl_C 0.58 47.0 4.36e-01 94.5% 82.4%
2825526 109.4.1.1300 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_8, TPR_16, TPR_19 0.57 45.0 4.43e-01 100.0% 79.2%
4998572 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.57 35.0 3.43e-01 87.7% 52.9%
3396301 190.1.1.5 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › Protamine_like 0.56 37.0 3.98e-01 82.2% 79.4%
5027940 4041.1.1.1 ↗ a+b complex topology › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › insertion domain in beta subunit of DNA dependent RNA-polymerase › RNA_pol_Rpb2_2 0.56 40.0 3.21e-01 79.5% 62.4%
4932241 2007.1.2.56 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › DUF116 0.55 42.0 3.22e-01 84.9% 82.2%
3699906 109.4.1.1522 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › PPR_2, PPR_3, TPR_24 0.54 47.0 3.87e-01 100.0% 62.9%
3506153 190.1.1.1 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.54 37.0 3.54e-01 80.8% 61.4%
3496552 190.1.1.3 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box_2 0.54 37.0 3.52e-01 80.8% 58.9%
3863510 190.1.1.3 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box_2 0.53 36.0 3.59e-01 75.3% 68.0%
4102066 190.1.1.1 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.53 36.0 3.25e-01 79.5% 50.5%
3802347 190.1.1.1 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.52 37.0 2.40e-01 78.1% 15.8%
3419147 190.1.1.1 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.52 37.0 3.45e-01 78.1% 58.9%
3506838 190.1.1.1 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.52 36.0 3.35e-01 80.8% 55.8%
3269300 190.1.1.1 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.52 36.0 3.50e-01 79.5% 62.4%
3176953 190.1.1.1 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.51 36.0 3.73e-01 78.1% 77.1%
3864894 190.1.1.1 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.51 35.0 3.40e-01 78.1% 62.4%
4344838 190.1.1.1 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.51 36.0 3.51e-01 79.5% 66.3%
3768093 190.1.1.1 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.51 36.0 3.21e-01 78.1% 50.5%
3992404 190.1.1.1 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.51 34.0 3.32e-01 80.8% 60.0%
3390901 190.1.1.1 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.51 36.0 2.66e-01 75.3% 48.8%
3720888 190.1.1.1 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.51 35.0 3.48e-01 76.7% 69.3%
3771624 190.1.1.1 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.51 35.0 3.21e-01 78.1% 53.0%
3323406 190.1.1.1 ↗ alpha arrays › HMG-box-like › HMG-box › HMG-box › HMG_box 0.50 34.0 2.53e-01 78.1% 24.8%
D2 medium residues 76-112_383-442
PDB
Domain cluster: representative
ECOD (6)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5039294 4038.1.1.1 ↗ alpha bundles › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Phage_portal 0.89 81.0 5.63e-01 96.9% 84.6%
4424174 4038.1.1.0 ↗ alpha bundles › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein 0.88 85.0 5.71e-01 100.0% 83.0%
4954546 4038.1.1.0 ↗ alpha bundles › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein 0.87 82.0 5.62e-01 100.0% 83.1%
4031453 4038.1.1.1 ↗ alpha bundles › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Phage_portal 0.78 70.0 4.98e-01 94.8% 85.9%
3604407 4038.1.1.0 ↗ alpha bundles › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein 0.74 68.0 4.91e-01 100.0% 84.2%
5018045 325.1.4.3 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Nicotinate/Quinolinate PRTase N-terminal domain-like › NAPRTase_N 0.52 39.0 3.40e-01 81.4% 81.3%
D3 medium residues 113-150_268-294
PDB
Domain cluster: representative
D4 medium residues 151-267
PDB
Domain cluster: rep: KC847113.1__AGK88024.1__PBP180_009__00009__D141-225
CATH (6)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3aj3A00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.55 42.0 3.27e-01 82.1% 97.4%
2r2dA00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.55 42.0 3.25e-01 82.1% 99.3%
2br6A01 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.54 42.0 3.37e-01 82.1% 99.1%
2mm0A00 2.10.70.110 Mainly Beta › Ribbon › Complement Module; domain 1 › 0.51 28.0 3.76e-01 90.6% 100.0%
2obaA00 3.30.479.10 Alpha Beta › 2-Layer Sandwich › Tetrahydropterin Synthase; Chain A › 6-pyruvoyl tetrahydropterin synthase/QueD 0.51 36.0 3.57e-01 70.9% 87.5%
4gnxC03 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.50 42.0 3.62e-01 89.7% 85.8%
ECOD (9)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4034031 4056.1.1.0 ↗ beta barrels › Barrel domain in upper collar protein › Barrel domain in upper collar protein › Barrel domain in upper collar protein 0.90 47.0 6.46e-01 94.0% 95.4%
4079740 4056.1.1.0 ↗ beta barrels › Barrel domain in upper collar protein › Barrel domain in upper collar protein › Barrel domain in upper collar protein 0.88 75.0 7.92e-01 96.6% 100.0%
4031151 4056.1.1.0 ↗ beta barrels › Barrel domain in upper collar protein › Barrel domain in upper collar protein › Barrel domain in upper collar protein 0.83 50.0 6.28e-01 100.0% 94.7%
5082482 4056.1.1.0 ↗ beta barrels › Barrel domain in upper collar protein › Barrel domain in upper collar protein › Barrel domain in upper collar protein 0.82 49.0 6.17e-01 100.0% 94.7%
3942998 4056.1.1.0 ↗ beta barrels › Barrel domain in upper collar protein › Barrel domain in upper collar protein › Barrel domain in upper collar protein 0.80 46.0 5.87e-01 99.1% 95.7%
4964819 4.15.1.2 ↗ beta barrels › SH3 › TrmB C-terminal domain-like › TrmB C-terminal domain-like › PF31112 0.55 37.0 3.84e-01 100.0% 71.8%
3895159 4.1.1.0 ↗ beta barrels › SH3 › SH3 › SH3 0.55 27.0 3.58e-01 89.7% 90.0%
4955607 3435.1.1.0 ↗ a+b two layers › Recombination-associated protein rdgC › Recombination-associated protein rdgC › Recombination-associated protein rdgC 0.53 39.0 3.27e-01 78.6% 75.8%
3337634 2.1.1.42 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › Rep_fac-A_C 0.50 43.0 3.90e-01 92.3% 95.6%
D5 medium residues 295-382
PDB
Domain cluster: representative
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4zosB00 3.30.70.100 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › 0.50 37.0 3.63e-01 79.5% 99.0%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4424174 4038.1.1.0 ↗ alpha bundles › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein › Alpha-helical domain in upper collar protein 0.75 69.0 4.68e-01 100.0% 31.7%
3592534 10.32.1.0 ↗ beta sandwiches › jelly-roll › Galactose-binding domain-like › Galactose-binding domain-like 0.56 43.0 3.50e-01 85.2% 71.1%
5035636 304.26.1.1 ↗ a+b two layers › Alpha-beta plaits › MTH1187/YkoF-like › MTH1187/YkoF-like › Thiamine_BP 0.51 41.0 3.97e-01 88.6% 99.0%