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highly_derived_D5-like_helicase-primase

Euk-Vir

Marseillevirus_marseillevirus

highly_derived_D5-like_helicase-primase__YP_003406787__Marseillevirus_marseillevirus__694581

Identity

Accession:
YP_003406787 ↗
Protein ID:
highly_derived_D5-like_helicase-primase
Kingdom:
euk

Quality

70.6 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Megaviricetes› Pimascovirales› Marseilleviridae› Marseillevirus› Marseillevirus_marseillevirus

TaxID: 694581

Cluster

Singleton — not in a non-trivial cluster

3D Structure

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Domains

high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.

D1 high residues 102-200_227-242
PDB
Domain cluster: rep: hypothetical_protein_H012_gp354__YP_007354538__Acanthamoeba_polyphaga_moumouvirus__1269028__D9-184
D2 high residues 265-368
PDB
D3 high residues 730-803
PDB
Domain cluster: rep: MK764448.1__QCW20633.1__X__00003__D396-466
D4 medium residues 27-98_201-226
PDB
D5 medium residues 424-501
PDB
D6 medium residues 502-554_678-727
PDB
Domain cluster: rep: highly_derived_D5-like_helicase-primase__YP_009238567__Brazilian_marseillevirus__1813599__D506-551_660-682_703-729
D7 medium residues 555-677
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF19263.6 best DUF5906 78.3 1.00e-21 91.9% 97.4%
CATH (36)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1tueD00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.78 69.0 5.78e-01 100.0% 57.9%
1svmA03 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.74 69.0 6.41e-01 100.0% 81.7%
3vkhA08 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.71 65.0 4.62e-01 98.4% 41.6%
3vkhB09 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.71 65.0 5.64e-01 98.4% 79.2%
3vkgA07 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.71 64.0 4.44e-01 96.7% 37.2%
3co5A00 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.68 52.0 5.05e-01 92.7% 73.9%
4akgA12 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.66 55.0 5.70e-01 95.9% 94.0%
4idhA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.63 58.0 4.84e-01 100.0% 75.5%
8bnsD01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.63 57.0 4.99e-01 100.0% 85.4%
5fhgA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.62 57.0 4.87e-01 100.0% 80.8%
1i4wA01 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.60 52.0 4.21e-01 98.4% 83.8%
2lndA00 3.40.50.11230 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.59 39.0 4.04e-01 97.6% 71.4%
7pujA01 3.20.20.80 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Glycosidases 0.59 51.0 3.89e-01 94.3% 81.7%
3nvaA01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.58 53.0 4.02e-01 100.0% 80.9%
4g56A01 3.20.20.150 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Divalent-metal-dependent TIM barrel enzymes 0.58 49.0 3.81e-01 92.7% 83.5%
1rifA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.58 51.0 4.40e-01 97.6% 77.1%
6abiA01 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.58 42.0 4.11e-01 93.5% 69.6%
3qfwB02 3.20.20.110 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Ribulose bisphosphate carboxylase, large subunit, C-terminal domain 0.57 50.0 4.03e-01 99.2% 84.4%
2gdqA02 3.20.20.120 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Enolase-like C-terminal domain 0.56 50.0 3.92e-01 99.2% 77.1%
3qz6A00 3.20.20.60 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Phosphoenolpyruvate-binding domains 0.56 50.0 3.94e-01 100.0% 86.9%
2oztA02 3.20.20.120 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Enolase-like C-terminal domain 0.55 46.0 3.97e-01 92.7% 84.2%
4w7sA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.55 45.0 3.99e-01 90.2% 90.3%
2ajrA01 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.54 46.0 3.64e-01 95.1% 73.6%
4d79A00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.54 47.0 3.79e-01 97.6% 74.9%
1q6oB00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.53 46.0 3.87e-01 95.1% 87.0%
2w2kA02 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.53 46.0 4.01e-01 97.6% 100.0%
5bo7B00 3.90.1480.20 Alpha Beta › Alpha-Beta Complex › sialyltransferase cstii, chain A › Glycosyl transferase family 29 0.53 46.0 3.56e-01 96.7% 62.7%
1mjfB02 3.40.50.150 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39 0.52 43.0 3.63e-01 91.1% 99.5%
5c3uA02 3.40.50.1100 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.52 32.0 3.52e-01 74.8% 76.0%
4l9yD00 3.20.20.60 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Phosphoenolpyruvate-binding domains 0.52 45.0 3.55e-01 95.9% 93.6%
1vjrA02 3.40.50.1000 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › HAD superfamily/HAD-like 0.52 42.0 4.46e-01 91.1% 100.0%
1zfjA00 3.20.20.70 Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Aldolase class I 0.52 46.0 3.12e-01 100.0% 68.5%
6ouvA03 3.40.50.920 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.51 36.0 3.56e-01 97.6% 68.9%
1y8qC00 3.40.50.720 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › NAD(P)-binding Rossmann-like Domain 0.50 43.0 3.28e-01 95.9% 85.2%
6vhyC01 3.40.50.12780 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ANL, N-terminal domain 0.50 44.0 3.14e-01 98.4% 50.3%
4dg8A01 3.40.50.12780 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › ANL, N-terminal domain 0.50 44.0 3.11e-01 98.4% 35.0%
ECOD (56)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3256248 2004.1.1.409 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF5906 0.94 62.0 5.86e-01 82.9% 58.6%
3253892 2004.1.1.409 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF5906 0.91 81.0 6.77e-01 100.0% 58.5%
5003620 2004.1.1.409 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF5906 0.83 77.0 5.47e-01 100.0% 36.1%
5029777 2004.1.1.409 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF5906 0.83 77.0 5.92e-01 100.0% 47.5%
5081314 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.83 76.0 5.81e-01 100.0% 46.2%
4959586 2004.1.1.409 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF5906 0.82 77.0 5.74e-01 100.0% 44.4%
3945876 2004.1.1.409 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF5906 0.81 74.0 5.63e-01 100.0% 44.9%
3954608 2004.1.1.409 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › DUF5906 0.81 76.0 5.80e-01 100.0% 47.7%
5011495 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.81 73.0 6.12e-01 100.0% 59.5%
2810781 8001.1.1.1 ↗ alpha arrays › N-terminal domain of large tumor antigen › N-terminal domain of large tumor antigen › N-terminal domain of large tumor antigen › PPV_E1_C 0.78 70.0 5.67e-01 100.0% 52.9%
4026992 1.1.9.0 ↗ beta barrels › cradle loop barrel › RIFT-related › PUA domain 0.77 71.0 4.59e-01 98.4% 27.3%
4033843 2004.1.1.313 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › VapE-like_dom 0.76 66.0 5.62e-01 100.0% 59.0%
3716216 2004.1.1.181 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_7 0.75 69.0 5.54e-01 100.0% 63.9%
3708220 2004.1.1.181 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_7 0.74 69.0 5.78e-01 100.0% 75.0%
4078827 2004.1.1.418 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MCM, Mg_chelatase 0.74 69.0 5.07e-01 100.0% 50.3%
3197159 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.73 68.0 4.58e-01 100.0% 36.0%
3702069 2004.1.1.181 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_7 0.73 68.0 5.57e-01 100.0% 69.0%
3695173 2004.1.1.46 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MCM 0.73 68.0 5.02e-01 100.0% 51.3%
4013468 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.73 68.0 5.13e-01 100.0% 56.0%
5025359 2004.1.1.46 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MCM 0.72 67.0 5.09e-01 100.0% 56.4%
3583688 2004.1.1.181 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_7 0.71 57.0 5.68e-01 83.7% 100.0%
None — 0.70 65.0 5.67e-01 100.0% 69.4%
4224436 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.70 64.0 5.00e-01 100.0% 90.4%
3925706 2004.1.1.93 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Dynein_heavy 0.70 59.0 5.89e-01 97.6% 89.6%
3665927 2004.1.1.415 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA, RuvB_N 0.70 65.0 5.34e-01 100.0% 74.3%
3377628 2004.1.1.46 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MCM 0.69 63.0 5.36e-01 97.6% 77.9%
4948046 2004.1.1.1203 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › RMMBL 0.67 52.0 4.52e-01 82.1% 100.0%
4890968 148.1.3.0 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.67 60.0 5.79e-01 96.7% 97.8%
4025422 2004.1.1.296 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MCM_bind 0.67 61.0 4.86e-01 100.0% 53.1%
3267799 2004.1.1.135 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › PIF1 0.67 61.0 5.04e-01 100.0% 85.1%
3605124 2004.1.1.135 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › PIF1 0.66 60.0 5.12e-01 100.0% 81.0%
4932834 2004.1.1.176 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Beta-Casp 0.66 53.0 4.42e-01 84.6% 93.7%
3472986 2004.1.1.296 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › MCM_bind 0.66 60.0 4.81e-01 100.0% 64.6%
4975660 247.1.1.0 ↗ a+b four layers › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase › Metallo-hydrolase/oxidoreductase 0.66 52.0 3.42e-01 83.7% 39.4%
3272236 2004.1.1.176 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Beta-Casp 0.65 50.0 4.24e-01 79.7% 99.5%
3778760 207.1.1.161 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_6, PF29265 0.65 53.0 4.03e-01 87.0% 76.1%
4890989 148.1.3.231 ↗ alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain › AAA_7 0.59 43.0 4.66e-01 74.8% 91.1%
3669005 207.1.1.95 ↗ beta duplicates or obligate multimers › Single-stranded right-handed beta-helix › Leucine-rich repeats › Leucine-rich repeats › LRR_14 0.59 48.0 3.32e-01 89.4% 56.3%
None — 0.58 51.0 3.67e-01 98.4% 79.9%
3519517 2004.1.1.30 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.58 50.0 4.34e-01 95.9% 87.7%
3812052 2004.1.1.0 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.57 52.0 4.25e-01 100.0% 82.2%
3970036 2003.1.5.0 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases 0.56 49.0 3.70e-01 98.4% 91.9%
4935010 2002.1.1.0 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.56 47.0 3.72e-01 92.7% 80.4%
3553500 2003.1.5.79 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Methyltransf_23 0.56 49.0 3.72e-01 98.4% 62.3%
3296268 2004.1.1.30 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.55 48.0 4.31e-01 97.6% 86.9%
2010840 2002.1.1.111 ↗ a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels › HpcH_HpaI 0.54 46.0 3.49e-01 95.9% 78.3%
3229893 2003.1.5.111 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Rsm22 0.54 48.0 3.57e-01 99.2% 84.8%
3266113 246.2.1.1 ↗ a+b four layers › Carbon-nitrogen hydrolase-like › Metallo-dependent phosphatases › Metallo-dependent phosphatases › Metallophos 0.53 47.0 3.55e-01 100.0% 93.3%
3096276 2003.1.1.37 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › NAD(P)-binding Rossmann-fold domains › 2-Hacid_dh_C 0.53 46.0 3.92e-01 97.6% 100.0%
3927414 2003.1.9.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Activating enzymes of the ubiquitin-like proteins › ThiF 0.53 47.0 3.05e-01 97.6% 94.1%
None — 0.52 42.0 2.89e-01 87.0% 56.0%
3230607 2003.1.9.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Activating enzymes of the ubiquitin-like proteins › ThiF 0.52 45.0 2.99e-01 96.7% 92.4%
5063286 2003.1.5.10 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › S-adenosyl-L-methionine-dependent methyltransferases › Fibrillarin 0.52 45.0 4.06e-01 96.7% 92.4%
3461386 2004.1.1.30 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Helicase_C 0.51 39.0 3.35e-01 100.0% 49.0%
3783934 2003.1.9.1 ↗ a/b three-layered sandwiches › Rossmann-like › Rossmann-related › Activating enzymes of the ubiquitin-like proteins › ThiF 0.51 44.0 2.91e-01 96.7% 92.3%
3688500 129.1.1.57 ↗ alpha arrays › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › 6-phosphogluconate dehydrogenase C-terminal domain-like › NAD_binding_4 0.50 44.0 3.01e-01 96.7% 82.0%