←Back to structures

MT374856.1__QKE55580.1__vBYpM23_00056__00056

Bact-Vir

MT374856.1__QKE55580.1__vBYpM23_00056__00056

Identity

Accession:
MT374856 ↗
Kingdom:
phage

Quality

89.4 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Muvirus› Yersinia_phage_vB_YpM_23

TaxID: 2736198

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 176-230
PDB
Domain cluster: rep: NC_079179.1__YP_010844740.1__QNH00_gp79__00079__D392-447
D2 medium residues 2-36
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF21446.4 best Gp34_trimer 29.7 1.10e-06 100.0% 27.0%
CATH (42)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7vyjB01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.76 58.0 3.70e-01 88.6% 17.2%
3venA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.76 57.0 3.52e-01 88.6% 38.6%
1vq8N00 3.30.420.100 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › 0.70 58.0 3.73e-01 100.0% 31.7%
1g5hA01 3.30.930.10 Alpha Beta › 2-Layer Sandwich › BirA Bifunctional Protein; domain 2 › Bira Bifunctional Protein; Domain 2 0.69 53.0 3.23e-01 100.0% 23.2%
3d2fA03 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.69 58.0 4.34e-01 100.0% 48.4%
3gvzA00 3.60.60.10 Alpha Beta › 4-Layer Sandwich › Penicillin V Acylase; Chain A › Penicillin V Acylase; Chain A 0.68 54.0 3.32e-01 100.0% 14.8%
6u5vB07 3.30.1120.100 Alpha Beta › 2-Layer Sandwich › Arylsulfatase, C-terminal domain › 0.68 58.0 3.98e-01 100.0% 30.2%
8ainB01 3.10.450.250 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › S. aureus uracil DNA glycosylase inhibitor 0.67 54.0 3.95e-01 100.0% 32.4%
4bfiB01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.64 50.0 3.66e-01 97.1% 32.1%
3u83A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.64 52.0 3.79e-01 100.0% 37.6%
2pndA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 52.0 3.57e-01 97.1% 31.1%
7xb6B01 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.62 46.0 3.01e-01 91.4% 44.9%
4eyyQ02 3.20.170.50 Alpha Beta › Alpha-Beta Barrel › ADP-ribosylation fold › Dot/Icm secretion system IcmQ, C-terminal domain 0.62 48.0 3.55e-01 100.0% 89.5%
3k1lA01 3.30.457.40 Alpha Beta › 2-Layer Sandwich › Copper Amine Oxidase; Chain A, domain 1 › 0.62 47.0 3.75e-01 100.0% 45.7%
2a1vA00 3.90.1150.30 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › 0.61 48.0 3.39e-01 100.0% 27.5%
3ooqF01 2.30.40.10 Mainly Beta › Roll › Urease, subunit C; domain 1 › Urease, subunit C, domain 1 0.61 51.0 3.85e-01 100.0% 45.7%
6ovnB01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.60 47.0 3.46e-01 100.0% 43.6%
1w7cA03 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.60 48.0 3.54e-01 100.0% 41.7%
7mxdX01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 44.0 3.16e-01 85.7% 72.3%
3hulB01 3.30.230.10 Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S5; domain 2 › 0.59 44.0 2.97e-01 85.7% 83.4%
2lssA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.59 42.0 3.61e-01 85.7% 98.6%
5z06B02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.59 41.0 3.28e-01 85.7% 62.0%
1c3kA00 2.100.10.30 Mainly Beta › Aligned Prism › Vitelline Membrane Outer Layer Protein I, subunit A › Jacalin-like lectin domain 0.58 40.0 2.81e-01 80.0% 22.4%
1cl8A00 3.40.580.10 Alpha Beta › 3-Layer(aba) Sandwich › ECO RI Endonuclease; Chain A › Eco RI Endonuclease, subunit A 0.58 43.0 2.75e-01 100.0% 78.2%
1eajB00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.58 47.0 3.35e-01 97.1% 34.2%
2fkcA01 3.40.1350.40 Alpha Beta › 3-Layer(aba) Sandwich › Trna Endonuclease; Chain: A, domain 1 › 0.56 42.0 3.23e-01 100.0% 53.6%
3jtzA00 3.30.160.390 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Integrase, DNA-binding domain 0.56 40.0 3.36e-01 85.7% 41.6%
1p9rA01 3.30.450.90 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › 0.56 39.0 2.97e-01 85.7% 25.2%
3bn0A00 3.30.1320.10 Alpha Beta › 2-Layer Sandwich › S16 Ribosomal Protein; Chain: A; › Ribosomal protein S16 0.55 46.0 3.48e-01 100.0% 41.1%
4bi3A01 3.90.1720.80 Alpha Beta › Alpha-Beta Complex › endopeptidase fold (from Nostoc punctiforme) › 0.55 39.0 3.10e-01 77.1% 34.1%
3kd9A02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.54 39.0 2.56e-01 100.0% 20.5%
1g29102 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.53 36.0 3.56e-01 80.0% 60.0%
6fndA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.52 36.0 2.48e-01 97.1% 17.2%
5hmaA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.52 38.0 3.00e-01 100.0% 32.7%
4bxsA02 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.52 39.0 2.68e-01 100.0% 40.0%
2kbnA00 2.40.50.140 Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins 0.51 38.0 2.93e-01 100.0% 58.7%
1tvdA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 42.0 3.09e-01 100.0% 45.7%
2v3aA03 3.30.390.120 Alpha Beta › 2-Layer Sandwich › Enolase-like; domain 1 › 0.51 38.0 3.33e-01 91.4% 84.4%
7essA01 3.30.420.140 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › YqgF/RNase H-like domain 0.51 39.0 2.83e-01 97.1% 83.3%
3wknF00 6.20.50.120 Special › Other non-globular › N-terminal domain of TfIIb › 0.51 37.0 3.63e-01 100.0% 76.1%
1autC01 2.40.10.10 Mainly Beta › Beta Barrel › Thrombin, subunit H › Trypsin-like serine proteases 0.51 41.0 2.89e-01 100.0% 75.4%
3cgbA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.50 42.0 2.78e-01 97.1% 75.2%
ECOD (31)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1503101 2484.1.1.30 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Carbam_trans_N 0.76 57.0 3.51e-01 88.6% 37.6%
3968442 2484.1.1.30 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Carbam_trans_N 0.75 60.0 3.71e-01 94.3% 37.7%
5029316 2484.1.1.30 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Carbam_trans_N 0.73 58.0 3.65e-01 94.3% 41.0%
3766391 77.1.1.2 ↗ beta meanders › open-sided beta-meander › Outer surface protein › Outer surface protein › FAM194 0.73 59.0 3.94e-01 100.0% 23.7%
3536554 77.1.1.2 ↗ beta meanders › open-sided beta-meander › Outer surface protein › Outer surface protein › FAM194 0.72 59.0 4.46e-01 100.0% 40.0%
3970247 9.11.1.0 ↗ beta barrels › Lipocalins/Streptavidin › YdhA-like › YdhA-like 0.72 57.0 4.05e-01 100.0% 29.1%
5079664 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.71 55.0 3.49e-01 94.3% 40.5%
4045704 2484.1.1.30 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Carbam_trans_N 0.71 53.0 3.32e-01 88.6% 14.9%
4935439 2002.1.1.83 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Amidohydro_1 0.71 61.0 3.45e-01 100.0% 86.8%
3589304 331.23.1.0 ↗ a+b two layers › TBP-like › Integrator IntS9/IntS11 C-terminal domain › Integrator IntS9/IntS11 C-terminal domain 0.70 55.0 4.54e-01 100.0% 48.0%
3872839 304.47.1.1 ↗ a+b two layers › Alpha-beta plaits › SEA domain › SEA domain › SEA 0.69 52.0 3.50e-01 88.6% 20.0%
3880209 913.1.1.0 ↗ few secondary structure elements › Hormone receptor domain (HRM, Pfam 02793) › Hormone receptor domain (HRM, Pfam 02793) › Hormone receptor domain (HRM, Pfam 02793) 0.68 51.0 4.74e-01 88.6% 62.0%
3985596 2002.1.1.152 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Amidohydro_3 0.68 56.0 3.24e-01 100.0% 87.1%
1442422 2484.1.1.69 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › Ribosomal_L18_c,Ribosomal_L5e 0.67 52.0 3.17e-01 100.0% 20.1%
3656236 5.1.3.135 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Kelch_1, Kelch_KLHDC2_KLHL20_DRC7, Beta-prop_ATRN-LZTR1 0.67 49.0 2.92e-01 97.1% 21.4%
3945724 2002.1.1.152 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › Amidohydro_3 0.67 55.0 3.16e-01 100.0% 88.1%
4024169 5.1.3.160 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 6-bladed › Kelch_KLHDC2_KLHL20_DRC7, Beta-prop_ATRN-LZTR1 0.64 44.0 2.49e-01 77.1% 6.0%
3602850 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.63 51.0 3.89e-01 100.0% 50.5%
3721757 386.1.1.0 ↗ few secondary structure elements › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers › beta-beta-alpha zinc fingers 0.62 47.0 4.17e-01 100.0% 56.9%
3313861 4325.1.1.10 ↗ mixed a+b and a/b › YegP-like › YegP-like › YegP-like › DUF659 0.62 45.0 4.02e-01 82.9% 56.4%
3633294 219.1.1.93 ↗ a+b complex topology › Cysteine proteinases-like › Cysteine proteinases › Cysteine proteinases › DUF6540 0.62 46.0 3.35e-01 100.0% 41.3%
3859041 11.1.1.99 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › V-set 0.61 51.0 3.41e-01 97.1% 30.7%
3921953 11.1.1.99 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › V-set 0.61 51.0 3.56e-01 97.1% 33.9%
5038693 213.1.1.17 ↗ a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › DUF1122 0.60 51.0 3.21e-01 100.0% 23.5%
3312424 2484.1.1.106 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › DUF659 0.58 45.0 2.66e-01 100.0% 92.2%
5014724 295.1.1.51 ↗ a+b two layers › ssDNA-binding transcriptional regulator domain-like › ssDNA-binding transcriptional regulator domain › ssDNA-binding transcriptional regulator domain › FtsQ_DivIB_C 0.55 46.0 3.42e-01 100.0% 52.0%
3383152 395.1.1.6 ↗ few secondary structure elements › Midkine-related › Midkine-related › Midkine-related › PF27637 0.53 37.0 3.89e-01 100.0% 86.7%
5000725 2.1.1.0 ↗ beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein 0.52 40.0 3.10e-01 100.0% 69.0%
3587399 331.1.1.2 ↗ a+b two layers › TBP-like › TATA-box binding protein-like › TATA-box binding protein-like › Rep_trans 0.51 39.0 2.69e-01 100.0% 81.8%
3665260 206.1.1.1 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase › Pkinase 0.51 38.0 2.47e-01 100.0% 64.4%
3642301 2007.1.2.4 ↗ a/b three-layered sandwiches › Flavodoxin-like › Class I glutamine amidotransferase-like › Periplasmic binding protein-like I › ANF_receptor 0.50 37.0 2.33e-01 88.6% 53.0%
D3 medium residues 45-95
PDB
Domain cluster: rep: OK254197.1__UIS66033.1__X__00020__D606-663
CATH (12)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3vsmA03 2.60.40.4340 Mainly Beta › Sandwich › Immunoglobulin-like › 0.72 51.0 4.14e-01 76.5% 40.4%
2x4jA01 2.30.30.600 Mainly Beta › Roll › SH3 type barrels. › 0.65 44.0 3.51e-01 70.6% 100.0%
3d79A01 3.10.450.120 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › Pre-PUA domain; domain 1 0.60 43.0 3.87e-01 78.4% 87.8%
1dhkB00 2.60.120.200 Mainly Beta › Sandwich › Jelly Rolls › 0.57 48.0 3.32e-01 100.0% 57.9%
1whzA00 3.30.920.30 Alpha Beta › 2-Layer Sandwich › Metal Transport, Frataxin; Chain A › Hypothetical protein. 0.55 38.0 3.47e-01 70.6% 73.9%
1onfA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.54 38.0 2.99e-01 76.5% 92.4%
1u5mA01 2.10.70.10 Mainly Beta › Ribbon › Complement Module; domain 1 › Complement Module, domain 1 0.53 33.0 3.55e-01 78.4% 83.3%
5x1yA02 3.50.50.60 Alpha Beta › 3-Layer(bba) Sandwich › FAD/NAD(P)-binding domain › FAD/NAD(P)-binding domain 0.52 36.0 2.85e-01 76.5% 92.6%
2r2dA00 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.52 40.0 2.60e-01 92.2% 75.7%
2a5hA03 6.20.120.40 Special › Other non-globular › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › 0.51 32.0 3.03e-01 86.3% 46.8%
1wubA00 2.40.128.110 Mainly Beta › Beta Barrel › Lipocalin › Lipid/polyisoprenoid-binding, YceI-like 0.51 41.0 2.97e-01 98.0% 72.2%
3udcA02 2.30.30.60 Mainly Beta › Roll › SH3 type barrels. › 0.50 36.0 3.64e-01 76.5% 78.0%
ECOD (16)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3980770 79.1.1.0 ↗ beta duplicates or obligate multimers › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain 0.93 86.0 5.79e-01 100.0% 30.9%
4928895 79.1.1.0 ↗ beta duplicates or obligate multimers › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain 0.82 65.0 4.02e-01 98.0% 16.4%
5075886 243.6.1.1 ↗ a+b two layers › Cystatin-like › Pre-PUA domain › Pre-PUA domain › DUF1947 0.74 52.0 4.70e-01 74.5% 84.3%
3633088 5.1.4.0 ↗ beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed 0.69 56.0 3.37e-01 92.2% 27.0%
4026913 243.6.1.4 ↗ a+b two layers › Cystatin-like › Pre-PUA domain › Pre-PUA domain › Pre-PUA 0.68 50.0 4.27e-01 80.4% 82.4%
4548121 243.6.1.9 ↗ a+b two layers › Cystatin-like › Pre-PUA domain › Pre-PUA domain › TGT_C2 0.64 39.0 3.56e-01 70.6% 42.9%
5003057 243.6.1.0 ↗ a+b two layers › Cystatin-like › Pre-PUA domain › Pre-PUA domain 0.63 44.0 4.02e-01 74.5% 87.1%
4526691 6043.1.1.0 ↗ a+b two layers › yfeY-like › yfeY-like › yfeY-like 0.62 43.0 3.98e-01 72.5% 67.7%
3939497 391.1.1.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module 0.62 39.0 4.25e-01 76.5% 75.0%
4953037 243.6.1.9 ↗ a+b two layers › Cystatin-like › Pre-PUA domain › Pre-PUA domain › TGT_C2 0.61 39.0 3.47e-01 70.6% 42.7%
3617611 391.1.1.20 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module › PSP94 0.61 38.0 4.12e-01 76.5% 75.0%
3801761 391.1.2.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › VWC domain-related 0.60 38.0 2.72e-01 76.5% 19.4%
1164615 243.6.1.1 ↗ a+b two layers › Cystatin-like › Pre-PUA domain › Pre-PUA domain › DUF1947 0.60 43.0 3.81e-01 78.4% 83.3%
4964361 502.1.1.3 ↗ a+b two layers › Anti-LPS factor/recA domain › Anti-LPS factor/recA domain › Anti-LPS factor/recA domain › DUF7348 0.54 38.0 3.49e-01 78.4% 55.7%
3837976 7570.1.1.1 ↗ a/b three-layered sandwiches › MurD-like peptide ligases, peptide-binding domain › MurD-like peptide ligases, peptide-binding domain › MurD-like peptide ligases, peptide-binding domain › Mur_ligase_C 0.53 43.0 3.01e-01 86.3% 53.8%
4299723 2.8.1.1 ↗ beta barrels › OB-fold › mu transposases-C › mu transposases-C › Mu-transpos_C 0.52 35.0 3.25e-01 72.5% 85.7%