←Back to structures

helicase_primase_complex_protein

Euk-Vir

Human_betaherpesvirus_6A

helicase_primase_complex_protein__NP_042936__Human_betaherpesvirus_6A__32603

Identity

Accession:
NP_042936 ↗
Protein ID:
helicase_primase_complex_protein
Kingdom:
euk

Quality

89.4 mean pLDDT

Taxonomy

Heunggongvirae› Peploviricota› Herviviricetes› Herpesvirales› Orthoherpesviridae› Roseolovirus› Human_betaherpesvirus_6A

TaxID: 32603

Cluster

View cluster (58 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 high residues 216-318_705-714
PDB
Domain cluster: rep: ORF56__YP_001129409__Human_gammaherpesvirus_8__37296__D254-341
CATH (24)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3a06B03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.69 44.0 4.89e-01 91.2% 83.0%
6mh4A03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.66 38.0 4.40e-01 71.7% 79.7%
2g8lA02 1.10.285.20 Mainly Alpha › Orthogonal Bundle › Glutamate Dehydrogenase; Chain A, domain 3 › Uncharacterised protein PF01937, DUF89, domain 2 0.64 38.0 4.68e-01 98.2% 100.0%
1r6bX03 1.10.8.60 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › 0.64 38.0 4.26e-01 83.2% 76.1%
1zp2A01 1.10.472.10 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Cyclin-like 0.62 36.0 3.62e-01 78.8% 53.9%
2aplA01 1.10.8.330 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › PG0816-like 0.61 37.0 4.43e-01 74.3% 100.0%
1xrhD01 1.10.1530.10 Mainly Alpha › Orthogonal Bundle › Hypothetical Oxidoreductase Yiak; Chain: A, domain 1 › Malate/L-lactate/L-sulpholactate dehydrogenase, four-helix barrel 0.58 34.0 3.59e-01 93.8% 63.1%
8anqA00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.57 45.0 3.60e-01 84.1% 45.5%
3no6A00 1.20.910.10 Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like 0.56 46.0 3.67e-01 89.4% 96.6%
3ejnA03 1.20.120.840 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SusD-like, tetratrico peptide repeats domain 0.56 37.0 3.76e-01 77.0% 67.6%
3gi7A00 1.20.1270.180 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.56 43.0 4.53e-01 83.2% 95.1%
5hiwA00 1.10.630.10 Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450 0.56 41.0 2.79e-01 76.1% 81.6%
2qffA00 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.55 30.0 3.51e-01 70.8% 77.0%
2iw3A02 1.20.1390.20 Mainly Alpha › Up-down Bundle › PWI domain › 0.55 35.0 3.79e-01 85.0% 78.9%
1f1eA00 1.10.20.10 Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A 0.54 45.0 4.16e-01 92.9% 94.0%
1bgvA03 1.10.285.10 Mainly Alpha › Orthogonal Bundle › Glutamate Dehydrogenase; Chain A, domain 3 › Glutamate Dehydrogenase, chain A, domain 3 0.53 30.0 3.55e-01 88.5% 81.6%
4hr1A00 1.20.1270.410 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.53 39.0 3.93e-01 78.8% 79.7%
1td6A03 1.10.472.40 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Hypothetical protein mg237 homolog; domain 3 0.53 37.0 4.05e-01 96.5% 91.3%
3ug9A02 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.53 43.0 3.48e-01 89.4% 99.6%
1z72A00 1.20.910.10 Mainly Alpha › Up-down Bundle › Heme Oxygenase; Chain A › Heme oxygenase-like 0.52 39.0 3.23e-01 79.6% 64.8%
3lcnB00 1.10.340.40 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Nuclear abundant poly(A) RNA-bind protein 2, N-terminal domain 0.51 41.0 4.40e-01 83.2% 100.0%
3r0qA02 2.70.160.11 Mainly Beta › Distorted Sandwich › Hnrnp arginine n-methyltransferase1 › Hnrnp arginine n-methyltransferase1 0.51 36.0 2.96e-01 72.6% 70.2%
7zdtD01 1.20.1560.10 Mainly Alpha › Up-down Bundle › ABC transporter transmembrane region fold › ABC transporter type 1, transmembrane domain 0.51 40.0 2.99e-01 87.6% 43.6%
2hujA00 1.20.120.440 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › YppE-like 0.50 37.0 3.63e-01 85.8% 70.4%
ECOD (22)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4959600 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.69 49.0 5.53e-01 92.9% 97.6%
4024704 3871.1.1.1 ↗ alpha duplicates or obligate multimers › PHIST › PHIST › PHIST › PRESAN 0.65 52.0 4.97e-01 86.7% 86.2%
4942070 5050.1.1.87 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › LPG_synthase_TM 0.58 41.0 3.15e-01 72.6% 74.8%
3939529 5067.1.1.3 ↗ alpha bundles › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Patched 0.58 51.0 4.05e-01 99.1% 75.4%
3402945 4953.1.1.0 ↗ beta barrels › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like › L-aspartase C-terminal domain-like 0.58 45.0 4.55e-01 85.8% 83.6%
3909467 180.1.1.0 ↗ alpha bundles › Acid phosphatase/Vanadium-dependent haloperoxidase › Acid phosphatase/Vanadium-dependent haloperoxidase › Acid phosphatase/Vanadium-dependent haloperoxidase 0.57 47.0 3.81e-01 90.3% 74.7%
4999359 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.56 42.0 4.59e-01 88.5% 98.9%
4499455 633.5.1.1 ↗ alpha bundles › Bromodomain-like › LemA-like › LemA-like › LemA 0.56 40.0 3.52e-01 85.8% 51.2%
3652633 3930.1.1.0 ↗ alpha bundles › Helical bundle insertion in helicase domains › Helical bundle in Hef helicase › Helical bundle in Hef helicase 0.56 39.0 3.76e-01 80.5% 63.1%
3589212 633.2.1.1 ↗ alpha bundles › Bromodomain-like › Carnobacteriocin B2 immunity protein › Carnobacteriocin B2 immunity protein › EntA_Immun 0.55 31.0 3.58e-01 77.0% 78.7%
3880538 632.1.1.28 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Families 57/38 glycoside transferase middle domain › Families 57/38 glycoside transferase middle domain › DUF2678 0.55 39.0 4.41e-01 77.0% 98.8%
3465074 611.9.1.4 ↗ alpha bundles › N-cbl like › Resistance protein (Rx) N-terminal domain › Resistance protein (Rx) N-terminal domain › Rx_N 0.53 42.0 4.06e-01 90.3% 76.0%
3490727 5050.1.1.6 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › OATP 0.52 43.0 3.46e-01 91.2% 45.0%
3578915 7073.1.1.1 ↗ alpha arrays › C-terminal domain of Malic enzyme › C-terminal domain of Malic enzyme › C-terminal domain of Malic enzyme › Malic_M 0.52 43.0 4.03e-01 90.3% 79.3%
3488980 632.7.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain 0.52 37.0 3.96e-01 80.5% 84.8%
4034431 632.15.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) › CompInhib_SCIN 0.52 36.0 4.11e-01 91.2% 98.8%
3578428 5067.1.1.0 ↗ alpha bundles › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain › Multidrug efflux transporter AcrB transmembrane domain 0.51 42.0 3.92e-01 92.0% 75.2%
3616671 604.1.1.155 ↗ alpha bundles › Spectrin repeat-like › Spectrin repeat › Spectrin repeat › PF29142 0.51 37.0 4.06e-01 87.6% 90.5%
3705545 3755.4.1.0 ↗ alpha bundles › YscO-like › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain › Phosphatidylinositol 3-kinase regulatory subunit inter-SH2 domain 0.51 46.0 3.99e-01 100.0% 93.1%
4188764 7014.1.1.1 ↗ alpha bundles › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › Undecaprenyl pyrophosphate phosphatase (UppP) transmembrane domain › BacA 0.51 31.0 3.09e-01 100.0% 56.7%
4472619 2004.1.1.483 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › UvrD-helicase, AAA_19, UvrD_C 0.50 41.0 2.43e-01 89.4% 67.4%
3721398 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.50 33.0 3.62e-01 73.5% 83.3%
D2 high residues 343-410
PDB
Domain cluster: representative
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3kdzA01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.62 48.0 3.50e-01 85.3% 56.0%
1gk3A01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.60 48.0 3.50e-01 88.2% 56.6%
7tqrA01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.60 47.0 3.50e-01 86.8% 57.7%
4n06A02 1.20.120.920 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CRISPR-associated endonuclease Cas1, C-terminal domain 0.59 49.0 3.32e-01 94.1% 52.7%
3w0oA02 3.90.1200.10 Alpha Beta › Alpha-Beta Complex › Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 › Aminoglycoside phosphotransferase (APH), C-terminal lobe 0.55 38.0 2.71e-01 72.1% 74.2%
1hqvA00 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.54 39.0 2.95e-01 77.9% 69.1%
2fsjA02 3.30.420.40 Alpha Beta › 2-Layer Sandwich › Nucleotidyltransferase; domain 5 › ATPase, nucleotide binding domain 0.52 45.0 3.56e-01 95.6% 81.9%
3unvA01 1.10.275.10 Mainly Alpha › Orthogonal Bundle › Fumarase C; Chain B, domain 1 › Fumarase/aspartase (N-terminal domain) 0.52 40.0 3.03e-01 89.7% 80.3%
1egaA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 38.0 2.93e-01 91.2% 32.0%
ECOD (21)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3654686 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.62 34.0 2.54e-01 100.0% 21.8%
4036353 4952.1.1.2 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › Lyase_aromatic 0.62 48.0 3.50e-01 85.3% 56.9%
3327906 3281.1.1.2 ↗ alpha complex topology › Sodium/proton antiporter subunits-like › Sodium/proton antiporter subunits-like › NADH-quinone oxidoreductase subunit L (NuoL)-related › Proton_antipo_M,Proton_antipo_N 0.60 50.0 2.97e-01 100.0% 36.8%
3936723 101.1.1.76 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Integrase_H2C2 0.60 36.0 3.12e-01 100.0% 37.3%
4000737 4.1.1.25 ↗ beta barrels › SH3 › SH3 › SH3 › PAZ 0.60 40.0 3.32e-01 70.6% 85.4%
4027323 2004.1.1.73 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MMR_HSR1 0.60 52.0 3.55e-01 97.1% 37.4%
3973686 4952.1.1.0 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like 0.59 47.0 3.41e-01 86.8% 55.9%
3236790 101.1.1.76 ↗ alpha arrays › HTH › HTH › Three-helical HTH › Integrase_H2C2 0.59 36.0 3.10e-01 100.0% 37.3%
5004081 3239.1.1.1 ↗ alpha complex topology › Cas1 › Cas1 › Cas1 › Cas_Cas1 0.57 44.0 2.89e-01 86.8% 47.5%
3741740 131.2.1.3 ↗ alpha complex topology › PDEase-like › Poly A polymerase C-terminal region-like › Poly A polymerase C-terminal region-like › PolyA_pol_RNAbd 0.55 46.0 3.12e-01 100.0% 51.3%
4942136 5081.1.1.1 ↗ alpha bundles › Rhomboid-like › Rhomboid-like › Rhomboid-like › Rhomboid 0.55 44.0 3.35e-01 94.1% 60.0%
3947868 2484.1.1.87 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › MreB-like_C 0.55 46.0 3.53e-01 95.6% 82.4%
4938105 5081.1.1.1 ↗ alpha bundles › Rhomboid-like › Rhomboid-like › Rhomboid-like › Rhomboid 0.54 44.0 3.37e-01 94.1% 50.6%
4945339 2484.1.1.0 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like 0.53 45.0 3.41e-01 95.6% 68.2%
1152766 7577.1.1.4 ↗ a/b three-layered sandwiches › PLP-dependent transferases › PLP-dependent transferases › PLP-dependent transferases › Pyridoxal_deC 0.53 46.0 2.97e-01 98.5% 64.9%
3651259 4001.1.1.4 ↗ a+b duplicates or obligate multimers › a+b domain in cullin-like proteins › a+b domain in cullin-like proteins › a+b domain in cullin-like proteins › Cullin_AB 0.53 45.0 4.05e-01 94.1% 77.9%
3478332 206.1.3.47 ↗ a+b complex topology › Protein kinase/SAICAR synthase/ATP-grasp › Protein kinase/SAICAR synthase/ATP-grasp › ATP-grasp › Citrate_synth_N 0.53 40.0 2.84e-01 88.2% 85.7%
5042736 5081.1.1.1 ↗ alpha bundles › Rhomboid-like › Rhomboid-like › Rhomboid-like › Rhomboid 0.52 41.0 3.08e-01 88.2% 56.2%
4029998 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.51 42.0 3.59e-01 91.2% 65.5%
4936459 2004.1.1.120 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ResIII 0.51 42.0 2.83e-01 100.0% 92.3%
148226 4952.1.1.2 ↗ alpha arrays › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › L-aspartase N-terminal domain-like › Lyase_aromatic 0.50 39.0 3.00e-01 92.6% 80.1%
D3 high residues 484-698
PDB
Domain cluster: rep: primase__YP_009345453__Noumeavirus__1955558__D12-194
D4 high residues 724-854
PDB
Domain cluster: rep: helicase-primase_primase_subunit__NP_944382__Psittacid_alphaherpesvirus_1__50294__D1138-1286
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF03121.21 best Herpes_UL52 78.4 4.20e-22 57.2% 96.0%
D5 medium residues 1-138
PDB
Domain cluster: rep: helicase-primase_primase_subunit__YP_010085930__Wood_mouse_herpesvirus__432370__D12-162
CATH (1)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1t95A02 1.10.10.900 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › SBDS protein C-terminal domain, subdomain 1 0.55 23.0 2.97e-01 89.1% 65.3%
D6 medium residues 139-215
PDB
Domain cluster: rep: helicase_primase_complex__NP_050224__Human_betaherpesvirus_6B__32604__D142-241
D7 medium residues 324-341_421-483
PDB
Domain cluster: representative