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DNA_helicase_PIF1,_ATP-dependent

Euk-Vir

Pandoravirus_macleodensis

DNA_helicase_PIF1,_ATP-dependent__YP_009480977__Pandoravirus_macleodensis__2107707

Identity

Accession:
YP_009480977 ↗
Protein ID:
DNA_helicase_PIF1,_ATP-dependent
Kingdom:
euk

Quality

74.7 mean pLDDT

Taxonomy

TaxID: 2107707

3D Structure

Domains

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

D1 high residues 37-219
PDB
Pfam (3)
AccessionNameScoreE-valueQ covHMM cov
PF05970.21 best PIF1 121.8 4.50e-35 92.3% 63.2%
PF13604.13 AAA_30 49.1 8.30e-13 84.7% 67.5%
PF13245.13 AAA_19 42.1 1.40e-10 79.8% 98.5%
D2 medium residues 271-368_429-452
PDB
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF21530.4 best Pif1_2B_dom 39.6 4.80e-10 36.1% 76.6%
CATH (3)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1ywhA01 2.10.60.10 Mainly Beta › Ribbon › CD59 › CD59 0.52 28.0 3.30e-01 93.4% 76.5%
6x4tA02 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.51 25.0 2.93e-01 80.3% 63.5%
2wdoA00 3.90.470.20 Alpha Beta › Alpha-Beta Complex › Ribosomal Protein L22; Chain A › 4'-phosphopantetheinyl transferase domain 0.51 30.0 3.01e-01 78.7% 56.9%
ECOD (32)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3707168 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.79 70.0 5.38e-01 93.4% 99.2%
3670014 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.76 49.0 6.05e-01 73.8% 100.0%
3363136 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.75 65.0 6.59e-01 89.3% 100.0%
3714141 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.75 62.0 5.91e-01 86.9% 100.0%
3321328 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.75 50.0 5.91e-01 84.4% 97.6%
3699523 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.75 62.0 5.53e-01 86.9% 100.0%
3255737 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.74 63.0 6.43e-01 89.3% 99.2%
3251896 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.74 64.0 6.58e-01 90.2% 100.0%
3491785 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.73 61.0 6.33e-01 86.9% 99.1%
4101587 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.73 60.0 6.52e-01 88.5% 100.0%
3670309 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.73 53.0 5.84e-01 96.7% 92.9%
3337833 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.72 52.0 6.00e-01 86.9% 100.0%
3267759 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.72 60.0 5.45e-01 87.7% 100.0%
3220797 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.71 59.0 6.35e-01 86.9% 100.0%
3594062 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.70 61.0 5.68e-01 90.2% 98.6%
3610097 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.70 60.0 5.72e-01 90.2% 97.9%
3708644 4.1.1.0 beta barrels › SH3 › SH3 › SH3 0.69 59.0 6.15e-01 90.2% 100.0%
3354687 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.69 49.0 4.94e-01 98.4% 73.3%
3816455 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.68 58.0 5.76e-01 89.3% 98.4%
3357239 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.68 57.0 5.18e-01 88.5% 77.8%
3932586 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.68 60.0 5.43e-01 95.1% 84.7%
3921963 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.67 59.0 5.74e-01 92.6% 99.3%
3668420 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.67 63.0 5.34e-01 100.0% 71.1%
3669214 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.67 62.0 6.13e-01 100.0% 99.2%
3332609 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.67 57.0 5.68e-01 90.2% 100.0%
3930014 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.66 59.0 5.30e-01 94.3% 83.7%
3363448 4.1.1.140 beta barrels › SH3 › SH3 › SH3 › Pif1_2B_dom 0.59 39.0 4.65e-01 85.2% 96.5%
3771215 382.1.1.0 few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.56 29.0 3.33e-01 88.5% 65.6%
3840554 382.1.1.0 few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.55 29.0 3.31e-01 93.4% 66.7%
3531342 382.1.1.0 few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like 0.55 30.0 3.38e-01 91.8% 67.8%
None 0.54 44.0 3.02e-01 98.4% 26.2%
4175824 387.1.1.0 few secondary structure elements › omega toxin-like › omega toxin-related › omega toxin-related 0.53 29.0 3.78e-01 91.0% 98.5%
D3 medium residues 369-428
PDB
Domain cluster: representative
CATH (14)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
2f93B00 1.10.287.470 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.73 49.0 5.30e-01 70.0% 92.2%
6gyhA00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.66 54.0 3.71e-01 93.3% 48.0%
3uqcB01 3.30.200.20 Alpha Beta › 2-Layer Sandwich › Phosphorylase Kinase; domain 1 › Phosphorylase Kinase; domain 1 0.65 36.0 3.15e-01 73.3% 35.5%
3hwcA03 1.20.140.10 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Butyryl-CoA Dehydrogenase, subunit A, domain 3 0.65 52.0 3.64e-01 91.7% 38.1%
3zbqA00 3.40.50.1440 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Tubulin/FtsZ, GTPase domain 0.59 52.0 3.29e-01 100.0% 72.7%
2kobA01 1.10.150.130 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Tyrosine recombinase, N-terminal domain 0.59 49.0 4.36e-01 98.3% 93.5%
1skoB00 3.30.450.30 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › Dynein light chain 2a, cytoplasmic 0.58 48.0 3.92e-01 93.3% 51.7%
4nphA02 1.20.1270.330 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.55 43.0 4.14e-01 91.7% 90.5%
6a95A01 1.10.238.10 Mainly Alpha › Orthogonal Bundle › Recoverin; domain 1 › EF-hand 0.55 46.0 3.67e-01 95.0% 50.0%
1e5rB02 1.10.1720.10 Mainly Alpha › Orthogonal Bundle › Proline Oxidase; Chain: A, Domain 2 › L-proline 3-hydroxylase, C-terminal domain 0.54 33.0 3.07e-01 100.0% 42.9%
1dcnA03 1.10.40.30 Mainly Alpha › Orthogonal Bundle › Ribonucleotide Reductase Protein R1; domain 1 › Fumarase/aspartase (C-terminal domain) 0.52 42.0 3.97e-01 95.0% 76.4%
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 0.51 44.0 3.89e-01 96.7% 95.5%
4gcvC00 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 0.51 39.0 3.11e-01 88.3% 86.5%
1xr4A02 3.40.1080.10 Alpha Beta › 3-Layer(aba) Sandwich › Glutaconate Coenzyme A-transferase › Glutaconate Coenzyme A-transferase 0.50 40.0 2.64e-01 90.0% 72.1%
ECOD (21)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3550485 904.1.1.22 few secondary structure elements › B-box zinc-binding domain-like › B-box zinc-binding domain › B-box zinc-binding domain › zf-B_box, TRIM_CC 0.83 56.0 3.76e-01 70.0% 20.5%
3485149 2004.1.1.19 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Ras 0.77 54.0 3.48e-01 71.7% 18.4%
3862031 2004.1.1.19 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Ras 0.77 53.0 3.42e-01 75.0% 16.9%
3479094 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.77 53.0 3.46e-01 71.7% 35.1%
4095036 109.4.1.22 alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Adaptin_N 0.75 52.0 3.01e-01 71.7% 10.2%
3258290 1128.1.1.1 alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR 0.69 52.0 4.90e-01 83.3% 70.7%
3518809 5.1.4.1 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40 0.68 57.0 3.68e-01 93.3% 20.4%
3276504 109.6.1.2 alpha superhelices › Repetitive alpha hairpins › Ras GEF › Ras GEF › RasGEF,RasGEF_N 0.68 51.0 3.11e-01 81.7% 48.1%
5005635 148.1.3.0 alpha arrays › Histone-like › Histone-related › AAA+ ATPase lid domain 0.67 50.0 5.19e-01 93.3% 89.1%
3714356 1128.1.1.1 alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR 0.67 57.0 5.13e-01 96.7% 95.3%
3886320 130.1.2.1 alpha arrays › LEM/SAP HeH motif-like › LEM/SAP HeH motif › ribosome-binding domain of Mdm38 › LETM1_RBD 0.65 61.0 4.17e-01 100.0% 88.6%
3615313 1128.1.1.2 alpha bundles › LYR protein › LYR protein › LYR protein › Complex1_LYR_2 0.64 50.0 4.54e-01 85.0% 62.5%
4554473 601.7.2.1 alpha bundles › Four-helical up-and-down bundle › HEPN › HEPN domain in CRISPR-associated protein Csx1 › Csx1_HEPN 0.63 55.0 4.70e-01 96.7% 74.7%
3249094 4291.1.1.1 beta barrels › Oxysterol-binding protein › Oxysterol-binding protein › Oxysterol-binding protein › Oxysterol_BP 0.63 54.0 3.27e-01 96.7% 63.3%
4961861 2008.1.1.0 a/b three-layered sandwiches › Restriction endonuclease-like › Restriction endonuclease-like › Restriction endonuclease-like 0.57 47.0 3.32e-01 88.3% 43.2%
4159554 101.1.2.73 alpha arrays › HTH › HTH › winged helix domain › RNA_pol_Rpc82 0.56 46.0 3.61e-01 95.0% 92.9%
4968033 2002.1.1.0 a/b barrels › TIM beta/alpha-barrel › TIM barrels › TIM barrels 0.54 43.0 2.51e-01 88.3% 81.7%
5021827 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.54 41.0 2.88e-01 85.0% 73.2%
3784412 5.1.4.44 beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › RCC1_2 0.54 37.0 2.25e-01 76.7% 9.4%
3705705 103.4.1.2 alpha arrays › RuvA-C › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein › Elongation factor TFIIS domain 2/ Kix domain of creb binding protein › TFIIS_M 0.53 45.0 3.72e-01 100.0% 67.0%
4215468 10.12.1.3 beta sandwiches › jelly-roll › Double-stranded beta-helix › Double-stranded beta-helix › Cupin_1 0.53 44.0 2.57e-01 90.0% 89.3%
D4 medium residues 453-534
PDB
Domain cluster: representative
CATH (7)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1gm5A05 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.64 43.0 3.52e-01 70.7% 66.0%
4qa9A00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.53 38.0 2.55e-01 79.3% 81.4%
1uxoA00 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 36.0 2.89e-01 74.4% 60.2%
3vkwA02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 37.0 3.19e-01 78.0% 47.9%
2xgjB02 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.51 39.0 2.96e-01 85.4% 44.0%
4obvA02 3.40.640.10 Alpha Beta › 3-Layer(aba) Sandwich › Aspartate Aminotransferase; domain 2 › Type I PLP-dependent aspartate aminotransferase-like (Major domain) 0.51 38.0 2.84e-01 82.9% 56.7%
5l8sA01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.51 36.0 2.66e-01 76.8% 59.9%
ECOD (25)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3605939 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.95 75.0 6.16e-01 81.7% 50.4%
3789466 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.95 75.0 5.86e-01 81.7% 43.2%
3600234 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.95 75.0 5.67e-01 81.7% 48.2%
3385675 2004.1.1.298 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Herpes_Helicase 0.94 74.0 5.94e-01 81.7% 51.7%
3267758 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.94 76.0 6.19e-01 82.9% 51.1%
3363137 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.94 75.0 6.16e-01 82.9% 50.4%
3777141 2004.1.1.298 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Herpes_Helicase 0.94 75.0 6.00e-01 82.9% 57.9%
3716782 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.93 73.0 6.10e-01 81.7% 61.5%
3882209 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.93 74.0 6.09e-01 82.9% 62.2%
3890170 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.93 73.0 5.92e-01 82.9% 47.9%
3610095 2004.1.1.298 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › Herpes_Helicase 0.92 74.0 5.61e-01 82.9% 48.2%
3891480 2004.1.1.135 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › PIF1 0.89 71.0 4.48e-01 82.9% 23.9%
3591776 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.88 69.0 5.39e-01 81.7% 52.9%
3242523 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.87 61.0 5.10e-01 72.0% 63.1%
3719002 2004.1.1.203 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › UvrD_C_2 0.86 67.0 5.56e-01 81.7% 50.4%
3601738 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.85 66.0 5.63e-01 81.7% 66.4%
3596401 2004.1.1.0 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases 0.82 64.0 5.33e-01 81.7% 50.4%
3653111 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 60.0 6.02e-01 78.0% 100.0%
3777175 2004.1.1.203 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › UvrD_C_2 0.76 53.0 4.13e-01 72.0% 37.1%
3710008 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 55.0 4.46e-01 80.5% 61.3%
2533813 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 0.61 51.0 3.77e-01 91.5% 66.5%
3690329 2004.1.1.473 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › ResIII, AAA_11 0.56 42.0 2.76e-01 80.5% 46.8%
3724988 2004.1.1.184 a/b three-layered sandwiches › P-loop domains-like › P-loop domains-related › P-loop containing nucleoside triphosphate hydrolases › AAA_11 0.54 40.0 2.68e-01 81.7% 46.8%
5009483 323.1.1.3 a+b complex topology › CoA-dependent acyltransferases › CoA-dependent acyltransferases › CoA-dependent acyltransferases › AMP-binding 0.53 42.0 3.10e-01 92.7% 67.0%
4291684 7512.1.1.42 a/b three-layered sandwiches › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › UDP-Glycosyltransferase/glycogen phosphorylase › GumK_N 0.50 35.0 2.67e-01 74.4% 94.1%