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helicase

Euk-Vir

Neodiprion_sertifer_nucleopolyhedrovirus

helicase__YP_025168__Neodiprion_sertifer_nucleopolyhedrovirus__111874

Identity

Accession:
YP_025168 ↗
Protein ID:
helicase
Kingdom:
euk

Quality

68.4 mean pLDDT

Taxonomy

Naldaviricetes› Lefavirales› Baculoviridae› Gammabaculovirus› Neodiprion_sertifer_nucleopolyhedrovirus

TaxID: 111874

Cluster

View cluster (45 members)

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 1044-1136
PDB
Domain cluster: rep: helicase__YP_667909__Neodiprion_abietis_NPV__204507__D1038-1129
D2 medium residues 293-456
PDB
Domain cluster: rep: DNA-helicase_1__YP_009091922__Erinnyis_ello_granulovirus__307444__D240-411
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4ip8A00 1.10.132.110 Mainly Alpha › Orthogonal Bundle › Topoisomerase I; Chain A, domain 4 › Serum amyloid A protein 0.56 34.0 4.09e-01 99.4% 93.3%
2qq8A02 1.10.8.270 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › putative rabgap domain of human tbc1 domain family member 14 like domains 0.53 27.0 3.33e-01 96.3% 79.2%
5kbwB00 1.10.1760.20 Mainly Alpha › Orthogonal Bundle › Arp2/3 complex 21 kDa subunit ARPC3 › 0.53 38.0 3.82e-01 75.0% 91.8%
5d0yA00 1.10.1760.20 Mainly Alpha › Orthogonal Bundle › Arp2/3 complex 21 kDa subunit ARPC3 › 0.52 38.0 3.90e-01 75.0% 95.5%
2qq8A03 1.10.472.80 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Ypt/Rab-GAP domain of gyp1p, domain 3 0.51 36.0 3.86e-01 97.6% 82.6%
ECOD (1)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
5001551 1075.1.2.1 ↗ alpha bundles › Type II ABC exporter transmembrane domain fold › Type II ABC exporter transmembrane domain-related › MacB transmembrane domain › FtsX 0.53 36.0 3.69e-01 70.7% 100.0%
D3 medium residues 562-617
PDB
Domain cluster: representative
CATH (47)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
7c1iA01 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.93 77.0 6.20e-01 89.3% 49.0%
1h6gA02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.93 77.0 5.75e-01 91.1% 39.5%
2hfsA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.93 74.0 5.27e-01 83.9% 32.2%
3gonA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.93 70.0 5.05e-01 78.6% 32.8%
4u1cA01 4.10.860.10 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › UVR domain 0.90 71.0 7.35e-01 83.9% 90.4%
4fymF00 3.40.50.2020 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.90 73.0 4.73e-01 87.5% 23.0%
1yzmA00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.89 67.0 7.29e-01 78.6% 95.7%
2gd5A00 6.10.140.1230 Special › Helix non-globular › Helix Hairpins › 0.89 81.0 5.90e-01 100.0% 39.4%
5jrcA00 1.20.58.2140 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.89 81.0 5.51e-01 100.0% 30.1%
1z0jB00 4.10.860.20 Few Secondary Structures › Irregular › DNA Excision Repair, Uvrb; Chain A › Rabenosyn, Rab binding domain 0.89 69.0 7.17e-01 82.1% 90.2%
4lctB00 1.25.40.570 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.87 80.0 4.74e-01 98.2% 16.1%
1sr2A00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.87 67.0 5.19e-01 83.9% 39.7%
4b6xA00 1.20.58.90 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.87 77.0 7.09e-01 98.2% 76.8%
3kwoA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.87 80.0 5.72e-01 100.0% 73.8%
2rklF00 1.20.5.420 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › Immunoglobulin FC, subunit C 0.87 73.0 7.56e-01 94.6% 100.0%
3t9jA00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.87 80.0 5.76e-01 100.0% 76.4%
1bgfA00 1.10.532.10 Mainly Alpha › Orthogonal Bundle › Transcription Factor, Stat-4 › STAT transcription factor, N-terminal domain 0.86 71.0 5.40e-01 89.3% 40.3%
3t46A00 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.86 68.0 6.06e-01 83.9% 62.7%
2oo2A00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.85 64.0 5.78e-01 80.4% 60.5%
1cpqA00 1.20.120.10 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c/b562 0.85 73.0 5.50e-01 98.2% 41.1%
1wcrA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.84 73.0 5.92e-01 96.4% 53.4%
1yvwA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.84 67.0 5.60e-01 85.7% 52.2%
3k59A06 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.83 59.0 6.38e-01 75.0% 100.0%
3nymA00 6.10.290.10 Special › Helix non-globular › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.83 74.0 5.68e-01 100.0% 60.5%
6he1B01 1.10.287.40 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Serine-tRNA synthetase, tRNA binding domain 0.82 64.0 6.09e-01 91.1% 71.9%
3ltoA02 3.30.70.890 Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › GHMP kinase, C-terminal domain 0.82 65.0 4.86e-01 85.7% 36.6%
1luwA01 1.10.287.990 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Fe,Mn superoxide dismutase (SOD) domain 0.81 72.0 6.93e-01 98.2% 92.2%
2yfaA02 1.20.1440.210 Mainly Alpha › Up-down Bundle › de novo design (two linked rop proteins) › 0.81 69.0 5.51e-01 98.2% 47.4%
2v5cA03 1.20.58.460 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Hyaluronidase post-catalytic domain-like 0.81 73.0 5.49e-01 100.0% 43.8%
1konA01 1.10.10.200 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › Integrase, N-terminal zinc-binding domain 0.81 58.0 5.41e-01 76.8% 61.8%
1wkbA03 1.10.730.10 Mainly Alpha › Orthogonal Bundle › Isoleucyl-tRNA Synthetase; Domain 1 › Isoleucyl-tRNA Synthetase; Domain 1 0.81 64.0 4.93e-01 85.7% 41.3%
1vmgA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.81 64.0 5.60e-01 85.7% 58.5%
1zs3A00 1.20.1260.10 Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle 0.80 71.0 5.00e-01 100.0% 64.3%
3r6nA02 1.20.58.1060 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.80 69.0 5.05e-01 100.0% 36.8%
2yxhA00 1.10.287.1080 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › MazG-like 0.79 64.0 5.02e-01 87.5% 44.2%
1aueB00 1.20.120.150 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › FKBP12-rapamycin binding domain 0.79 60.0 5.10e-01 83.9% 50.0%
3l8rA00 1.20.58.80 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › Phosphotransferase system, lactose/cellobiose-type IIA subunit 0.79 69.0 5.69e-01 100.0% 54.9%
3tdvA02 3.90.1200.10 Alpha Beta › Alpha-Beta Complex › Aminoglycoside 3'-phosphotransferase; Chain: A, domain 2 › Aminoglycoside phosphotransferase (APH), C-terminal lobe 0.79 66.0 4.47e-01 94.6% 27.2%
4h63K00 1.10.287.3490 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.76 65.0 5.53e-01 100.0% 58.2%
1cgnA00 1.20.120.10 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c/b562 0.76 66.0 5.13e-01 98.2% 45.2%
1o9gA02 1.10.287.540 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.75 52.0 5.61e-01 73.2% 95.3%
4u72A01 1.20.58.480 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.71 63.0 4.16e-01 96.4% 24.3%
4gmnA00 1.25.10.10 Mainly Alpha › Alpha Horseshoe › Leucine-rich Repeat Variant › Leucine-rich Repeat Variant 0.69 56.0 3.22e-01 92.9% 9.8%
2f93B00 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.68 51.0 5.29e-01 80.4% 92.2%
4ar9A02 1.10.390.20 Mainly Alpha › Orthogonal Bundle › Neutral Protease; domain 2 › 0.66 45.0 3.34e-01 71.4% 28.2%
5b1aC01 1.10.287.70 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.60 49.0 4.71e-01 100.0% 86.8%
4fvmA06 1.10.287.690 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › B family DNA polymerase, finger domain 0.59 43.0 4.52e-01 83.9% 97.9%
ECOD (45)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3709352 4177.1.1.0 ↗ alpha duplicates or obligate multimers › BAR/IMD domain-like › BAR/IMD domain-like › BAR/IMD domain-like 0.93 86.0 6.04e-01 100.0% 36.1%
3976258 616.1.1.0 ↗ alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain 0.93 78.0 7.89e-01 89.3% 89.1%
5009299 304.1.1.1 ↗ a+b two layers › Alpha-beta plaits › GHMP Kinase, C-terminal domain › GHMP Kinase, C-terminal domain › GHMP_kinases_C 0.92 75.0 5.45e-01 89.3% 35.6%
5036797 3291.1.1.0 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related 0.91 84.0 5.81e-01 100.0% 32.9%
3738041 192.5.1.1 ↗ alpha bundles › Long alpha-hairpin › HR1 repeat › HR1 repeat › HR1 0.91 85.0 7.22e-01 100.0% 65.9%
4514051 192.7.1.2 ↗ alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N 0.91 84.0 6.46e-01 100.0% 48.7%
4963289 3877.1.1.0 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.90 78.0 5.23e-01 98.2% 27.4%
3230775 192.1.1.25 ↗ alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain › VPS18_RING_C 0.90 78.0 6.07e-01 92.9% 47.3%
4962838 225.1.1.3 ↗ a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › HATPase_c 0.90 82.0 5.36e-01 100.0% 26.5%
3560750 192.17.1.0 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.89 81.0 7.53e-01 100.0% 81.4%
3186698 192.17.1.0 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.89 82.0 7.20e-01 100.0% 70.0%
4930198 605.1.1.2 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › H-kinase_dim 0.89 79.0 7.70e-01 96.4% 88.3%
4942853 2004.1.1.146 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ATPase 0.89 81.0 4.80e-01 100.0% 14.7%
5051638 605.1.1.2 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › H-kinase_dim 0.89 77.0 7.85e-01 94.6% 96.4%
4000811 3291.1.1.1 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Snf7 0.89 81.0 6.04e-01 100.0% 43.8%
4469597 192.17.1.11 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › UVR 0.89 65.0 6.58e-01 80.4% 78.2%
None — 0.89 69.0 4.02e-01 82.1% 20.7%
5051215 192.11.1.1 ↗ alpha bundles › Long alpha-hairpin › C-terminal UvrC-binding domain of UvrB › C-terminal UvrC-binding domain of UvrB › UVR 0.89 65.0 5.80e-01 80.4% 57.3%
3240245 192.17.1.1 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like › Rbsn 0.88 68.0 7.24e-01 83.9% 92.0%
5024703 3877.1.1.0 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.88 74.0 4.99e-01 91.1% 26.8%
5013251 3291.1.1.195 ↗ alpha bundles › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › Charged multivesicular body protein 3 (CHMP3)-related › H-kinase_dim 0.87 79.0 5.71e-01 98.2% 38.5%
3560590 3755.3.1.142 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin › FAM186A-B_C 0.87 80.0 5.70e-01 100.0% 61.3%
1406322 109.4.1.2096 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_6, TPR_19, PF30363, PF30475 0.87 79.0 4.39e-01 100.0% 9.0%
5025189 192.17.1.0 ↗ alpha bundles › Long alpha-hairpin › Rabenosyn-5 Rab-binding domain-like › Rabenosyn-5 Rab-binding domain-like 0.87 68.0 6.92e-01 83.9% 85.5%
4883518 304.1.1.0 ↗ a+b two layers › Alpha-beta plaits › GHMP Kinase, C-terminal domain › GHMP Kinase, C-terminal domain 0.86 65.0 6.09e-01 80.4% 66.2%
5015169 3877.1.1.0 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.86 77.0 5.32e-01 98.2% 31.8%
4930709 3877.1.1.0 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.86 78.0 5.21e-01 98.2% 28.2%
4936633 3877.1.1.0 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.85 76.0 5.03e-01 98.2% 26.3%
4958554 304.48.1.3 ↗ a+b two layers › Alpha-beta plaits › Adenylyl and guanylyl cyclase catalytic domain-like › Adenylyl and guanylyl cyclase catalytic domain-like › DNA_pol_B 0.85 76.0 4.89e-01 98.2% 33.2%
3943105 2004.1.1.5 ↗ a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ABC_tran 0.84 75.0 4.30e-01 100.0% 11.1%
3262528 138.1.1.0 ↗ alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain 0.84 76.0 6.68e-01 98.2% 87.5%
5011606 2484.1.1.124 ↗ mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › OrfB_IS605 0.84 75.0 5.08e-01 98.2% 29.5%
3965106 605.1.1.4 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase › HisKA_3 0.84 75.0 6.78e-01 98.2% 76.0%
3477749 192.1.1.0 ↗ alpha bundles › Long alpha-hairpin › GreA transcript cleavage protein, N-terminal domain › GreA transcript cleavage protein, N-terminal domain 0.82 72.0 6.65e-01 100.0% 77.1%
5039485 3877.1.1.0 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.82 68.0 4.59e-01 96.4% 25.5%
4949471 3877.1.1.0 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.81 70.0 4.81e-01 92.9% 29.7%
4960168 3877.1.1.0 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.81 71.0 5.02e-01 98.2% 32.7%
4973347 515.1.1.4 ↗ alpha arrays › Transcription factor STAT-4 N-domain › Transcription factor STAT-4 N-domain › Transcription factor STAT-4 N-domain › EMC3_TMCO1 0.81 68.0 4.74e-01 91.1% 31.8%
4988301 3877.1.1.0 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.81 72.0 5.21e-01 98.2% 37.3%
5053329 223.2.1.0 ↗ a+b three layers › Profilin-like › profilin-like › profilin-like 0.81 67.0 5.14e-01 91.1% 41.7%
5043090 5058.1.1.16 ↗ alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › MS_channel_1st_1 0.76 65.0 5.77e-01 94.6% 67.5%
4947128 4336.1.1.15 ↗ alpha duplicates or obligate multimers › YheA/YmcA-like › YheA/YmcA-like › YheA/YmcA-like › EMC3_TMCO1 0.75 66.0 4.71e-01 98.2% 34.5%
3470615 3877.1.1.0 ↗ alpha bundles › Membrane protein insertase YidC-related › Membrane protein insertase YidC-related › Membrane protein insertase YidC 0.75 63.0 4.05e-01 91.1% 22.5%
2750143 3758.1.1.1 ↗ alpha bundles › Bacterial hemolysins-like › Bacterial hemolysins › Bacterial hemolysins › Bacillus_HBL 0.74 62.0 4.42e-01 100.0% 31.3%
4961158 5076.2.1.3 ↗ alpha complex topology › Mitochondrial ADP/ATP carrier-like › Putative sulfate permease CysZ › Putative sulfate permease CysZ › DUF4013 0.69 53.0 3.60e-01 85.7% 22.7%
D4 medium residues 618-737_750-767
PDB
D5 medium residues 811-967_991-1007
PDB
Domain cluster: rep: MN062720.1__QDP45567.1__SEA_FUZZBUSTER_83__00083__D568-722_747-764
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF04735.17 best Baculo_helicase 79.9 1.30e-22 98.9% 12.4%