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VV_D5-like_helicase

Euk-Vir

Pithovirus_sibericum

VV_D5-like_helicase__YP_009000916__Pithovirus_sibericum__1450746

Identity

Accession:
YP_009000916 ↗
Protein ID:
VV_D5-like_helicase
Kingdom:
euk

Quality

70.1 mean pLDDT

Taxonomy

Bamfordvirae› Nucleocytoviricota› Megaviricetes› Pimascovirales› Pithoviridae› Alphapithovirus› Pithovirus_sibericum

TaxID: 1450746

Cluster

View cluster (27 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 795-872
PDB
Domain cluster: rep: D5_family_NTPase_ATPase__YP_010084866__Shrimp_hemocyte_iridescent_virus__2039780__D809-878
CATH (23)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3dplC03 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.69 55.0 5.43e-01 93.6% 80.7%
3o2pE00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.68 56.0 5.42e-01 97.4% 80.2%
3x1oA00 1.20.120.1790 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.66 54.0 4.43e-01 97.4% 47.7%
2fe3B01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.64 52.0 5.05e-01 97.4% 80.0%
2ysrA00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.64 55.0 5.04e-01 97.4% 87.6%
2qbyA03 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.63 57.0 5.46e-01 100.0% 87.8%
2ph7A01 1.10.3400.10 Mainly Alpha › Orthogonal Bundle › af_2093 domain like fold › af_2093 domain like 0.62 54.0 4.65e-01 98.7% 69.4%
3cuqA02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.61 53.0 5.27e-01 97.4% 96.3%
2m7bA00 1.10.10.1920 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › 0.61 50.0 5.11e-01 96.2% 92.2%
2xubA02 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.60 51.0 4.91e-01 97.4% 81.5%
5hvqC01 3.90.1150.220 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › 0.60 51.0 5.15e-01 96.2% 93.8%
3mwmA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.60 48.0 4.96e-01 98.7% 93.3%
2xigA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.58 50.0 4.80e-01 97.4% 82.4%
3eyyA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.58 45.0 4.43e-01 97.4% 78.0%
7o1rA01 1.10.489.10 Mainly Alpha › Orthogonal Bundle › Chloroperoxidase › Chloroperoxidase-like 0.57 47.0 3.56e-01 92.3% 66.8%
7znvA01 1.10.489.10 Mainly Alpha › Orthogonal Bundle › Chloroperoxidase › Chloroperoxidase-like 0.57 49.0 3.75e-01 98.7% 51.8%
7zclA01 1.10.489.10 Mainly Alpha › Orthogonal Bundle › Chloroperoxidase › Chloroperoxidase-like 0.57 46.0 3.52e-01 92.3% 66.2%
1cf7B00 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.56 48.0 4.75e-01 98.7% 96.3%
5nl9A01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.56 47.0 4.62e-01 96.2% 95.2%
1mzbA01 1.10.10.10 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Winged helix-like DNA-binding domain superfamily/Winged helix DNA-binding domain 0.53 46.0 4.60e-01 97.4% 97.6%
7q37A01 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.53 42.0 3.15e-01 89.7% 66.4%
2be4A03 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.53 45.0 4.41e-01 100.0% 86.4%
3cx5B02 3.30.830.10 Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like 0.52 41.0 3.58e-01 91.0% 87.4%
ECOD (33)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3498779 101.1.2.34 ↗ alpha arrays › HTH › HTH › winged helix domain › RFX_DNA_binding 0.75 68.0 6.64e-01 100.0% 100.0%
3480455 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.74 67.0 6.70e-01 98.7% 100.0%
4967393 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.73 59.0 6.17e-01 97.4% 95.7%
4991793 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.73 60.0 4.25e-01 98.7% 30.7%
3249045 101.1.15.0 ↗ alpha arrays › HTH › HTH › HAT1, C-terminal domain 0.72 66.0 5.52e-01 100.0% 60.0%
3696367 101.1.1.0 ↗ alpha arrays › HTH › HTH › Three-helical HTH 0.71 52.0 5.30e-01 85.9% 80.0%
3608085 101.1.2.127 ↗ alpha arrays › HTH › HTH › winged helix domain › Cullin_Nedd8 0.70 57.0 5.40e-01 96.2% 73.4%
3607562 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.68 55.0 5.73e-01 94.9% 98.6%
3708443 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.67 60.0 5.74e-01 98.7% 85.6%
4955909 101.1.2.101 ↗ alpha arrays › HTH › HTH › winged helix domain › Cdc6_C 0.66 61.0 5.37e-01 100.0% 80.9%
5035389 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.64 54.0 5.30e-01 98.7% 85.9%
3435809 101.1.2.386 ↗ alpha arrays › HTH › HTH › winged helix domain › WH_DRP 0.64 56.0 4.98e-01 97.4% 78.2%
3816427 101.1.2.386 ↗ alpha arrays › HTH › HTH › winged helix domain › WH_DRP 0.63 55.0 5.00e-01 98.7% 71.4%
3575508 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.63 54.0 4.78e-01 96.2% 76.5%
3362715 101.1.2.386 ↗ alpha arrays › HTH › HTH › winged helix domain › WH_DRP 0.63 54.0 5.33e-01 97.4% 91.8%
3216952 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.63 53.0 5.25e-01 96.2% 89.4%
3550851 101.1.2.86 ↗ alpha arrays › HTH › HTH › winged helix domain › SMC_Nse1 0.62 53.0 5.22e-01 96.2% 90.6%
3315625 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.62 56.0 4.44e-01 100.0% 62.6%
4946290 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.62 45.0 4.88e-01 97.4% 93.8%
3925904 101.1.2.57 ↗ alpha arrays › HTH › HTH › winged helix domain › EAP30 0.61 53.0 4.15e-01 98.7% 45.7%
3719981 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.61 52.0 4.88e-01 97.4% 77.9%
3962321 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.60 53.0 4.93e-01 100.0% 91.0%
5029501 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.60 52.0 4.37e-01 98.7% 61.4%
3743672 101.1.2.186 ↗ alpha arrays › HTH › HTH › winged helix domain › ASH2L-like_WH 0.60 52.0 4.95e-01 100.0% 95.8%
3954639 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.60 51.0 5.04e-01 96.2% 90.6%
3675610 101.1.2.386 ↗ alpha arrays › HTH › HTH › winged helix domain › WH_DRP 0.59 52.0 4.72e-01 100.0% 79.0%
3808288 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.59 51.0 4.76e-01 98.7% 77.0%
4521366 101.1.2.12 ↗ alpha arrays › HTH › HTH › winged helix domain › DEP 0.58 49.0 4.48e-01 97.4% 83.6%
4978412 101.1.2.48 ↗ alpha arrays › HTH › HTH › winged helix domain › PadR 0.58 48.0 3.81e-01 97.4% 42.3%
4092408 102.1.1.119 ↗ alpha arrays › HhH/H2TH › SAM/DNA-glycosylase › SAM domain-like › DUF4332 0.57 44.0 4.49e-01 84.6% 88.0%
3647082 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.57 44.0 4.20e-01 97.4% 72.6%
4927083 101.1.2.0 ↗ alpha arrays › HTH › HTH › winged helix domain 0.57 46.0 4.38e-01 97.4% 75.5%
4024283 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.56 43.0 4.38e-01 88.5% 82.7%
D2 medium residues 1-57_182-192
PDB
D3 medium residues 58-167_193-203_230-265
PDB
D4 medium residues 289-371
PDB
Domain cluster: rep: putative_primase__YP_009506829__Tunisvirus_fontaine2__1421067__D281-379
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF08707.17 best PriCT_2 28.1 3.00e-06 94.0% 98.7%
CATH (17)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
3h20A04 1.10.1240.50 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › 0.66 50.0 4.96e-01 81.9% 89.9%
2dlaA01 1.20.930.50 Mainly Alpha › Up-down Bundle › Transcription Elongation Factor S-II; Chain A › 0.66 54.0 4.37e-01 90.4% 72.5%
4jgiA01 1.10.1240.10 Mainly Alpha › Orthogonal Bundle › Methyltransferase, Methionine Synthase (B12-binding Domains); Chain A, domain 1 › Methionine synthase domain 0.63 46.0 4.67e-01 75.9% 100.0%
8gtzA03 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.63 45.0 3.55e-01 74.7% 70.2%
1sxjE03 1.20.272.10 Mainly Alpha › Up-down Bundle › Zinc Finger, Delta Prime; domain 3 › 0.62 48.0 4.60e-01 84.3% 85.6%
5iduA01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.61 47.0 4.24e-01 84.3% 88.3%
1sz9C00 1.25.40.90 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.60 44.0 3.81e-01 79.5% 49.3%
1gd8A00 3.90.1030.10 Alpha Beta › Alpha-Beta Complex › 50s Ribosomal Protein L17; Chain: A, › Ribosomal protein L17 0.57 41.0 3.84e-01 77.1% 75.2%
8an5A01 3.30.460.40 Alpha Beta › 2-Layer Sandwich › Beta Polymerase; domain 2 › 0.57 41.0 3.17e-01 75.9% 36.5%
1iwpG02 1.10.1510.20 Mainly Alpha › Orthogonal Bundle › Hypothetical Protein Yqey; Chain: A; domain1 › Propanediol/glycerol dehydratase, small subunit 0.56 38.0 3.71e-01 73.5% 62.4%
3b9qA01 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.55 41.0 4.07e-01 79.5% 74.2%
2r5sA02 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.55 39.0 3.90e-01 75.9% 75.0%
3beeA00 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.55 37.0 3.66e-01 73.5% 63.7%
2lvfA00 1.10.110.10 Mainly Alpha › Orthogonal Bundle › Hydrophobic Seed Protein › Plant lipid-transfer and hydrophobic proteins 0.55 40.0 3.73e-01 80.7% 80.7%
4a2qA01 1.10.533.10 Mainly Alpha › Orthogonal Bundle › Death Domain, Fas › Death Domain, Fas 0.53 37.0 3.58e-01 72.3% 66.7%
2yikA00 1.50.10.10 Mainly Alpha › Alpha/alpha barrel › Glycosyltransferase › 0.52 44.0 2.84e-01 100.0% 92.5%
3k9iA01 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.51 36.0 3.42e-01 75.9% 61.2%
ECOD (15)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4950149 3896.1.2.0 ↗ alpha duplicates or obligate multimers › Intramembrane CDP-DAG synthetase-related › Intramembrane CDP-DAG synthetase-related › Intramembrane CDP-archaeol synthase 0.63 48.0 3.86e-01 84.3% 91.4%
3928494 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.60 45.0 3.09e-01 81.9% 37.2%
4479932 181.1.1.1 ↗ alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins › SRP54_N 0.59 41.0 4.04e-01 81.9% 67.8%
3594667 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.59 42.0 3.59e-01 78.3% 47.3%
3833652 4133.1.1.1 ↗ alpha arrays › Emsy N terminal (ENT) domain-like › Emsy N terminal (ENT) domain-like › Emsy N terminal (ENT) domain-like › ENT 0.58 40.0 4.12e-01 72.3% 82.7%
4471463 3455.1.1.0 ↗ alpha arrays › WY-domain in RXLR effectors › WY-domain in RXLR effectors › WY-domain in RXLR effectors 0.58 43.0 4.01e-01 79.5% 68.6%
4034377 4982.1.1.2 ↗ alpha arrays › KaiA/RbsU domain-like › KaiA/RbsU domain › KaiA/RbsU domain › RsbU_N 0.56 40.0 3.90e-01 74.7% 80.0%
4658028 140.1.1.0 ↗ 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 0.55 42.0 2.50e-01 80.7% 93.0%
3617171 109.4.1.271 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › FAN1_TPR 0.55 40.0 3.30e-01 79.5% 41.8%
None — 0.54 41.0 3.18e-01 81.9% 56.8%
3289370 101.1.1.300 ↗ alpha arrays › HTH › HTH › Three-helical HTH › HTH_30 0.54 39.0 3.73e-01 77.1% 67.0%
3174278 5048.1.1.1 ↗ alpha complex topology › Aquaporin-like › Aquaporin-like › Aquaporin-like › MIP 0.53 43.0 2.94e-01 89.2% 61.8%
3926730 101.1.10.0 ↗ alpha arrays › HTH › HTH › Cyclin-like 0.53 41.0 3.86e-01 86.7% 89.5%
4002510 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.52 38.0 3.62e-01 79.5% 72.0%
3906253 101.1.10.0 ↗ alpha arrays › HTH › HTH › Cyclin-like 0.51 38.0 3.45e-01 81.9% 80.0%
D5 medium residues 372-558
PDB
Domain cluster: representative
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF08706.17 best D5_N 30.1 7.90e-07 85.0% 83.0%
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2xrhA00 1.20.120.1430 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HP0721 helical bundle 0.54 24.0 3.12e-01 90.9% 72.0%
2lseA00 1.20.120.1360 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.52 23.0 3.07e-01 90.9% 74.3%
2x6hA03 1.10.1070.11 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, Domain 5 › Phosphatidylinositol 3-/4-kinase, catalytic domain 0.50 36.0 3.56e-01 72.7% 94.0%
D6 medium residues 559-597_722-794
PDB
Domain cluster: rep: conserved_D5_family_helicase-primase__YP_009094637__Melbournevirus__1560514__D702-732_758-807
D7 medium residues 598-721
PDB
Domain cluster: rep: MN062720.1__QDP45567.1__SEA_FUZZBUSTER_83__00083__D568-722_747-764