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DNA_packaging_terminase_subunit_2

Euk-Vir

Canid_alphaherpesvirus_1

DNA_packaging_terminase_subunit_2__YP_009252256__Canid_alphaherpesvirus_1__170325

Identity

Accession:
YP_009252256 ↗
Protein ID:
DNA_packaging_terminase_subunit_2
Kingdom:
euk

Quality

78.5 mean pLDDT

Taxonomy

Heunggongvirae› Peploviricota› Herviviricetes› Herpesvirales› Orthoherpesviridae› Varicellovirus› Canid_alphaherpesvirus_1

TaxID: 170325

Cluster

View cluster (77 members)

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 medium residues 6-123
PDB
Domain cluster: rep: transport_protein__YP_004207847__Cricetid_gammaherpesvirus_2__1605972__D1-97
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01366.24 best PRTP 82.4 3.00e-23 94.9% 16.8%
CATH (44)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2iakA01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.77 68.0 5.65e-01 93.2% 83.3%
3r6nB01 1.20.58.60 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.76 62.0 4.94e-01 85.6% 49.6%
1wcrA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.75 59.0 6.31e-01 83.9% 100.0%
1fpoC02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.74 51.0 5.77e-01 74.6% 92.3%
3nvoB02 1.20.58.340 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Magnesium transport protein CorA, transmembrane region 0.74 59.0 5.95e-01 84.7% 100.0%
3l8rA00 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 57.0 6.11e-01 83.1% 99.0%
2ntxA01 1.20.58.2010 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › PRONE domain, subdomain 1 0.72 57.0 4.71e-01 84.7% 59.5%
1i6zA00 1.20.58.120 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › BAG domain 0.72 57.0 5.50e-01 84.7% 83.7%
3uo2B02 1.20.1280.20 Mainly Alpha › Up-down Bundle › Monooxygenase › HscB, C-terminal domain 0.71 46.0 5.27e-01 76.3% 91.7%
2i0mA01 1.20.58.220 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphate transport system protein phou homolog 2; domain 2 0.70 57.0 5.93e-01 86.4% 100.0%
4rngC00 1.20.1280.290 Mainly Alpha › Up-down Bundle › Monooxygenase › 0.70 47.0 5.41e-01 78.0% 97.6%
3frrA00 1.20.1260.60 Mainly Alpha › Up-down Bundle › Ferritin › Vacuolar protein sorting-associated protein Ist1 0.68 49.0 4.20e-01 74.6% 77.4%
3qweA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.67 48.0 3.69e-01 73.7% 78.5%
6xz3A01 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.67 54.0 5.44e-01 85.6% 86.3%
1fewA00 1.20.58.70 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.66 53.0 4.65e-01 85.6% 79.2%
3u8vA00 1.20.120.660 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › IL-4 antagonist (De novo design) like domain 0.66 40.0 4.59e-01 87.3% 85.5%
1xdpA01 1.20.58.310 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Polyphosphate kinase N-terminal domain 0.65 48.0 5.04e-01 76.3% 92.4%
1wdzA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.65 46.0 3.74e-01 73.7% 81.4%
3iqcA00 1.20.120.340 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Flagellar protein FliS 0.65 47.0 4.74e-01 89.8% 74.8%
1x04A00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.64 46.0 3.90e-01 74.6% 80.0%
4wpeA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.64 46.0 3.53e-01 74.6% 76.7%
2d1lA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.64 46.0 3.59e-01 73.7% 76.3%
3pltA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.63 45.0 3.72e-01 73.7% 93.5%
3ok8A00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.63 45.0 3.66e-01 72.9% 81.3%
2q12A00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.62 44.0 3.52e-01 73.7% 71.1%
1sziA02 1.20.120.340 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Flagellar protein FliS 0.62 53.0 5.08e-01 94.1% 84.7%
1xwjA01 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.61 48.0 4.70e-01 85.6% 80.0%
2v0oB00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.59 43.0 3.29e-01 74.6% 74.9%
3ns4A00 1.10.357.110 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Vacuolar protein sorting-associated protein 53, C-terminus 0.59 50.0 4.22e-01 94.1% 62.4%
3u3iA02 1.20.58.1110 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.58 44.0 4.57e-01 78.8% 86.1%
5gl7A01 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.58 49.0 4.39e-01 92.4% 72.9%
2wb7A03 1.20.120.870 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › pT26-6p, five-helical bundle domain 0.58 44.0 4.21e-01 80.5% 100.0%
3ezuA01 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.57 40.0 3.53e-01 72.9% 79.1%
2v5cA03 1.20.58.460 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Hyaluronidase post-catalytic domain-like 0.57 46.0 4.47e-01 91.5% 79.2%
7kypB01 1.10.3470.10 Mainly Alpha › Orthogonal Bundle › ABC transporter involved in vitamin B12 uptake, BtuC › ABC transporter involved in vitamin B12 uptake, BtuC 0.56 45.0 3.46e-01 86.4% 70.4%
4nooB00 1.10.8.1160 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.55 41.0 4.52e-01 83.1% 95.8%
4xxiA00 1.10.490.20 Mainly Alpha › Orthogonal Bundle › Globin-like › Phycocyanins 0.54 38.0 3.57e-01 72.0% 76.9%
5ojcA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.53 39.0 3.62e-01 78.0% 90.9%
3g9gA00 1.20.1270.60 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › Arfaptin homology (AH) domain/BAR domain 0.52 42.0 3.28e-01 85.6% 79.6%
2zy9A03 1.10.357.20 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › SLC41 divalent cation transporters, integral membrane domain 0.52 41.0 3.66e-01 84.7% 57.5%
3s84A02 1.20.120.20 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Apolipoprotein 0.51 37.0 3.32e-01 73.7% 80.9%
6v9zA02 1.20.1560.10 Mainly Alpha › Up-down Bundle › ABC transporter transmembrane region fold › ABC transporter type 1, transmembrane domain 0.51 45.0 3.33e-01 99.2% 86.2%
4zvaA00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.51 36.0 3.38e-01 73.7% 84.6%
4uiqB00 1.10.490.10 Mainly Alpha › Orthogonal Bundle › Globin-like › Globins 0.51 36.0 3.33e-01 72.9% 83.0%
ECOD (30)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3237761 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.80 62.0 6.70e-01 81.4% 99.0%
4003767 603.1.1.136 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins › HB_ELP1 0.78 64.0 5.59e-01 86.4% 72.4%
3993692 604.1.1.179 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › PF30976 0.76 57.0 6.06e-01 78.0% 94.3%
3288367 150.8.1.1 ↗ alpha bundles › Ferritin/Heme oxygenase/4-helical cytokines › PPE › PPE › PPE 0.74 51.0 4.45e-01 70.3% 93.5%
3250233 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.71 62.0 5.28e-01 94.1% 63.2%
3872051 5086.1.1.0 ↗ alpha bundles › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins › helical hairpin of HlyD-like secretion proteins 0.68 55.0 4.57e-01 85.6% 98.5%
3208120 633.23.1.22 ↗ alpha bundles › Bromodomain-like › Claudin › Claudin › MARVEL 0.68 52.0 4.81e-01 82.2% 78.7%
3909538 604.1.1.0 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat 0.67 52.0 5.47e-01 80.5% 99.0%
4032683 604.5.1.2 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › PhoU 0.67 60.0 4.95e-01 100.0% 93.5%
3253934 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.66 52.0 5.23e-01 83.9% 87.5%
3862625 601.1.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin 0.66 53.0 5.07e-01 89.0% 72.9%
4023478 633.10.1.0 ↗ alpha bundles › Bromodomain-like › IVS-encoded protein-like › IVS-encoded protein-like 0.66 55.0 4.72e-01 89.8% 68.9%
5027736 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.65 55.0 4.86e-01 94.1% 65.6%
3790887 174.1.1.32 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Transmemb_17 0.65 50.0 4.75e-01 84.7% 67.6%
4946592 604.5.1.1 ↗ alpha bundles › Spectrin repeat-like › PhoU-like (Pfam 01895) › PhoU-like (Pfam 01895) › PhoU_div 0.64 57.0 4.72e-01 98.3% 91.4%
3536875 4177.1.1.1 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › FCH 0.64 46.0 3.45e-01 74.6% 75.8%
3227805 5001.1.1.63 ↗ alpha bundles › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › Family A G protein-coupled receptor-like › 7TM_GPCR_Srab 0.63 51.0 3.86e-01 89.0% 81.0%
3220199 174.1.1.1 ↗ few secondary structure elements › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin transmembrane domain › Tetraspanin 0.63 47.0 4.31e-01 83.1% 59.4%
3740490 4177.1.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.63 45.0 3.62e-01 73.7% 82.2%
3595254 4177.1.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.63 44.0 3.67e-01 72.0% 80.0%
4986068 5082.1.1.1 ↗ alpha bundles › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation efflux protein transmembrane domain-like › Cation_efflux 0.61 55.0 4.65e-01 100.0% 91.0%
3971983 3758.2.1.0 ↗ alpha bundles › Bacterial hemolysins-like › Biopolymer transport protein ExbB › Biopolymer transport protein ExbB 0.61 55.0 4.22e-01 100.0% 85.1%
3582458 4177.1.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.59 44.0 3.37e-01 78.8% 72.2%
3667486 633.7.1.0 ↗ alpha bundles › Bromodomain-like › Bacillus cereus metalloprotein-like › Bacillus cereus metalloprotein-like 0.58 46.0 4.02e-01 85.6% 65.4%
3603032 622.1.1.0 ↗ alpha bundles › YvfG-like › HSC20 (HSCB), C-terminal oligomerisation domain › HSC20 (HSCB), C-terminal oligomerisation domain 0.58 40.0 4.62e-01 71.2% 100.0%
None — 0.56 43.0 3.18e-01 82.2% 96.2%
3760483 603.1.1.0 ↗ alpha bundles › STAT-like › t-snare proteins › t-snare proteins 0.54 47.0 4.03e-01 95.8% 76.8%
3943210 5079.1.1.1 ↗ alpha duplicates or obligate multimers › Magnesium transporter MgtE membrane domain › Magnesium transporter MgtE membrane domain › Magnesium transporter MgtE membrane domain › MgtE 0.52 41.0 3.55e-01 85.6% 58.9%
3864210 2004.1.1.250 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Kinesin,Microtub_bd 0.51 42.0 2.75e-01 90.7% 25.7%
4002015 4177.1.1.3 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like › Arfaptin 0.51 46.0 3.72e-01 100.0% 90.2%
D2 medium residues 124-191_508-529
PDB
Domain cluster: rep: DNA_packaging_terminase_subunit_2__YP_007969816__Elephantid_betaherpesvirus_1__146015__D118-183_479-495
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01366.24 best PRTP 64.0 1.10e-17 77.8% 10.7%
D3 medium residues 228-239_370-417
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF01366.24 best PRTP 35.6 4.40e-09 95.0% 6.7%
CATH (2)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2xmxA01 1.20.1440.280 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.58 44.0 3.38e-01 81.7% 66.4%
2w3qA02 3.40.1050.10 Alpha Beta › 3-Layer(aba) Sandwich › Beta-carbonic Anhydrase; Chain A › Carbonic anhydrase 0.55 48.0 3.49e-01 96.7% 42.7%
ECOD (3)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3950427 633.6.1.2 ↗ alpha bundles › Bromodomain-like › Acyl-CoA dehydrogenase C-terminal domain-like › Acyl-CoA dehydrogenase C-terminal domain-like › ACOX 0.67 46.0 3.32e-01 71.7% 80.0%
3957580 2003.1.2.24 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › FAD/NAD(P)-binding domain › Pyr_redox_2 0.54 41.0 3.09e-01 83.3% 72.3%
4613951 306.7.1.1 ↗ a+b two layers › Glucose permease domain IIB-like › Trigger factor ribosome-binding domain › Trigger factor ribosome-binding domain › Trigger_N 0.54 40.0 3.20e-01 80.0% 41.6%
D4 medium residues 240-270_322-369
PDB
Domain cluster: rep: DNA_packaging_terminase_subunit_2__YP_009054935__Equid_alphaherpesvirus_3__80341__D240-271_328-381
D5 medium residues 530-569_681-749
PDB
Domain cluster: rep: terminase_subunit_2__YP_009179297__Elephant_endotheliotropic_herpesvirus_4__548914__D513-536_648-697