←Back to structures

NC_021073.1__YP_007878100.1__VPDG_00128__00127

Bact-Vir

NC_021073.1__YP_007878100.1__VPDG_00128__00127

Identity

Accession:
NC_021073 ↗
Kingdom:
phage

Quality

90.8 mean pLDDT

Taxonomy

Heunggongvirae› Uroviricota› Caudoviricetes› Vibrio_phage_henriette_12B8

TaxID: 573174

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 77-140
PDB
Domain cluster: representative
CATH (40)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1w99A01 1.20.190.10 Mainly Alpha › Up-down Bundle › Delta-Endotoxin; domain 1 › Pesticidal crystal protein, N-terminal domain 0.86 73.0 5.25e-01 93.8% 42.2%
3nbxX03 1.20.58.1510 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.83 75.0 6.37e-01 98.4% 81.2%
3gnlB02 1.10.287.1890 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.82 60.0 5.92e-01 76.6% 77.9%
1yxrA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.78 63.0 5.99e-01 90.6% 74.3%
7smtA02 1.20.58.390 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Neurotransmitter-gated ion-channel transmembrane domain 0.76 65.0 4.71e-01 93.8% 36.8%
1cunA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.76 64.0 5.48e-01 93.8% 81.4%
4oydB00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.75 64.0 5.27e-01 95.3% 77.8%
4kb2A01 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.75 63.0 5.31e-01 93.8% 77.1%
2guzB00 1.10.287.110 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › DnaJ domain 0.75 50.0 5.07e-01 76.6% 69.2%
6ko5A02 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.75 65.0 4.23e-01 100.0% 69.5%
1x8zB00 1.20.140.40 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Invertase/pectin methylesterase inhibitor family protein 0.74 67.0 5.06e-01 100.0% 59.2%
1dd5A01 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.74 63.0 5.32e-01 95.3% 80.7%
6xxvC00 1.10.132.20 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Ribosome-recycling factor 0.73 63.0 5.29e-01 96.9% 80.2%
4wzxA01 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.73 62.0 5.87e-01 92.2% 78.7%
3layF00 1.20.120.1490 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.73 52.0 4.85e-01 75.0% 74.4%
3pe0A02 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.72 60.0 5.13e-01 93.8% 74.5%
2uubT00 1.20.58.110 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Ribosomal protein S20 0.72 56.0 4.95e-01 90.6% 56.6%
1j1jA02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.72 60.0 5.52e-01 93.8% 71.8%
3zgzA04 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.72 62.0 4.54e-01 98.4% 37.9%
3axjB02 1.20.58.200 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Translin; domain 2 0.71 57.0 5.31e-01 93.8% 72.9%
3rwlA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.70 61.0 3.75e-01 98.4% 29.7%
3h36A00 1.10.10.400 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Polyribonucleotide nucleotidyltransferase, RNA-binding domain 0.69 60.0 5.65e-01 96.9% 80.8%
2rldA00 1.20.1440.60 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 23S rRNA-intervening sequence 0.69 60.0 5.04e-01 100.0% 73.7%
2yfaA02 1.20.1440.210 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.69 59.0 4.97e-01 100.0% 82.8%
3t6gB00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.69 58.0 4.63e-01 95.3% 86.6%
4aifA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.69 55.0 4.18e-01 90.6% 38.2%
4cs9B02 1.20.120.1350 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Pneumovirus matrix protein 2 (M2), zinc-binding domain 0.68 47.0 3.95e-01 100.0% 43.0%
4it4A02 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.68 58.0 5.18e-01 93.8% 67.0%
3u3iA02 1.20.58.1110 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 56.0 4.71e-01 92.2% 64.8%
5jrcA00 1.20.58.2140 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.67 57.0 4.19e-01 100.0% 75.8%
1pkfA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.66 60.0 3.64e-01 100.0% 32.5%
3czhA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.66 58.0 3.52e-01 100.0% 25.8%
4cs9C00 1.20.120.1350 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Pneumovirus matrix protein 2 (M2), zinc-binding domain 0.65 44.0 3.32e-01 100.0% 27.9%
2juaA00 1.20.1480.30 Mainly Alpha › Up-down Bundle › hypothetical protein mp506/mpn330, domain 1 › Designed four-helix bundle protein 0.63 53.0 4.67e-01 100.0% 78.4%
4u7iA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.62 52.0 4.67e-01 95.3% 75.3%
2qyuA02 1.25.40.300 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Putative secreted effector protein 0.61 50.0 3.61e-01 93.8% 31.3%
3upuA03 2.30.30.780 Mainly Beta › Roll › SH3 type barrels. › 0.60 49.0 3.92e-01 90.6% 54.2%
4j0eA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.57 52.0 3.61e-01 100.0% 39.6%
3fmcC01 3.40.630.10 Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Zn peptidases 0.54 46.0 3.04e-01 96.9% 22.4%
1f68A00 1.20.920.10 Mainly Alpha › Up-down Bundle › Histone Acetyltransferase; Chain A › Bromodomain-like 0.52 46.0 3.95e-01 100.0% 78.6%
ECOD (28)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3458224 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.87 75.0 6.21e-01 93.8% 60.0%
3272287 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.84 73.0 6.20e-01 93.8% 78.0%
3876247 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.83 71.0 5.74e-01 93.8% 76.7%
4096596 223.1.1.0 ↗ a+b three layers › Profilin-like › sensor domains › sensor domains 0.81 56.0 3.30e-01 71.9% 53.0%
5014600 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.81 68.0 5.37e-01 90.6% 47.2%
3801401 109.3.1.2 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › Ank,Ank_2 0.81 61.0 3.80e-01 79.7% 29.0%
3910599 604.1.1.7 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › SR_plectin_7 0.81 69.0 5.61e-01 93.8% 74.8%
4452814 140.1.1.7 ↗ alpha bundles › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases › DALR_2 0.80 67.0 5.23e-01 95.3% 43.7%
3877040 1134.1.1.0 ↗ alpha bundles › C-terminal helical domain of alanine-tRNA ligase › C-terminal helical domain of alanine-tRNA ligase › Eukaryotic C-Ala helical domain 0.80 65.0 6.14e-01 93.8% 74.7%
3522858 604.1.1.1 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › Spectrin 0.78 66.0 5.60e-01 93.8% 81.9%
3472984 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.78 55.0 3.99e-01 75.0% 92.6%
4030521 604.12.1.2 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain › Vta1 0.78 59.0 5.60e-01 92.2% 69.3%
3707968 604.12.1.0 ↗ alpha bundles › Spectrin repeat-like › MIT domain › MIT domain 0.77 64.0 5.30e-01 92.2% 53.9%
3498448 604.3.1.0 ↗ alpha bundles › Spectrin repeat-like › BAG domain › BAG domain 0.77 64.0 6.01e-01 93.8% 78.8%
3267735 109.4.1.598 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Mak10 0.76 70.0 4.52e-01 100.0% 50.2%
3419839 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.76 66.0 4.39e-01 100.0% 67.7%
4303951 601.54.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › low CO2-inducible protein LCI1 › low CO2-inducible protein LCI1 0.74 67.0 5.33e-01 100.0% 70.4%
3302941 5081.1.1.1 ↗ alpha bundles › Rhomboid-like › Rhomboid-like › Rhomboid-like › Rhomboid 0.73 64.0 4.50e-01 98.4% 40.5%
3438721 5081.1.1.1 ↗ alpha bundles › Rhomboid-like › Rhomboid-like › Rhomboid-like › Rhomboid 0.73 64.0 4.48e-01 98.4% 40.5%
4344857 650.1.1.2 ↗ alpha bundles › Chaperone J-domain › Chaperone J-domain › Chaperone J-domain › Pam16 0.72 58.0 5.30e-01 89.1% 78.8%
3597397 604.6.1.0 ↗ alpha bundles › Spectrin repeat-like › GAT-like domain › GAT-like domain 0.71 63.0 4.38e-01 100.0% 63.3%
3585155 109.3.1.170 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › Ank, Ank_4 0.69 61.0 3.87e-01 100.0% 30.5%
4420321 7015.1.1.0 ↗ alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain 0.68 60.0 4.85e-01 100.0% 68.0%
3524431 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.67 54.0 4.48e-01 93.8% 64.8%
3484907 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.67 54.0 4.54e-01 93.8% 70.0%
3758339 5086.1.1.65 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › USHBP1_PDZ-bd 0.67 55.0 4.88e-01 89.1% 67.8%
3999880 109.3.1.2 ↗ alpha superhelices › Repetitive alpha hairpins › Ankyrin repeat › Ankyrin repeat › Ank,Ank_2 0.66 58.0 4.00e-01 96.9% 45.6%
3757569 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.63 51.0 4.14e-01 93.8% 77.7%
D2 medium residues 1-71
PDB
Domain cluster: representative