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F-box_domain_containing_protein

Euk-Vir

Pandoravirus_quercus

F-box_domain_containing_protein__YP_009483288__Pandoravirus_quercus__2107709

Identity

Accession:
YP_009483288 ↗
Protein ID:
F-box_domain_containing_protein
Kingdom:
euk

Quality

68.5 mean pLDDT

Taxonomy

Pandoravirus› Pandoravirus_quercus

TaxID: 2107709

Cluster

View cluster (6 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 152-333
PDB
Domain cluster: rep: F-box_domain_containing_protein__YP_009483832__Pandoravirus_quercus__2107709__D62-270
CATH (5)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4r1kB00 3.10.450.50 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.61 35.0 3.99e-01 80.2% 74.3%
3my2A00 2.60.450.10 Mainly Beta › Sandwich › lipopolysaccharide transport protein A fold › Lipopolysaccharide (LPS) transport protein A like domain 0.59 40.0 4.73e-01 75.8% 97.6%
3wjcA00 2.40.128.20 Mainly Beta › Beta Barrel › Lipocalin › Calycin beta-barrel core domain 0.55 36.0 3.88e-01 79.7% 75.8%
3pquA02 2.40.160.90 Mainly Beta › Beta Barrel › Porin › 0.54 38.0 3.91e-01 72.0% 87.0%
3hi7B02 3.10.450.40 Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, › 0.51 34.0 3.94e-01 73.6% 94.5%
ECOD (18)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3719689 77.2.1.1 ↗ beta meanders › open-sided beta-meander › Histone H3 K4-specific methyltransferase SET7/9-N › Histone H3 K4-specific methyltransferase SET7/9-N › MORN 0.90 44.0 6.29e-01 79.1% 93.7%
3772693 77.3.1.3 ↗ beta meanders › open-sided beta-meander › CPAP G-box domain › CPAP G-box domain › MORN 0.86 46.0 4.37e-01 76.9% 46.2%
4030599 77.2.1.1 ↗ beta meanders › open-sided beta-meander › Histone H3 K4-specific methyltransferase SET7/9-N › Histone H3 K4-specific methyltransferase SET7/9-N › MORN 0.86 50.0 5.73e-01 94.0% 74.8%
3416878 77.3.1.3 ↗ beta meanders › open-sided beta-meander › CPAP G-box domain › CPAP G-box domain › MORN 0.83 45.0 4.56e-01 78.6% 53.5%
3539857 77.2.1.1 ↗ beta meanders › open-sided beta-meander › Histone H3 K4-specific methyltransferase SET7/9-N › Histone H3 K4-specific methyltransferase SET7/9-N › MORN 0.81 47.0 4.44e-01 78.6% 49.8%
3600811 77.2.1.0 ↗ beta meanders › open-sided beta-meander › Histone H3 K4-specific methyltransferase SET7/9-N › Histone H3 K4-specific methyltransferase SET7/9-N 0.79 45.0 5.82e-01 78.6% 91.3%
3597404 77.3.1.0 ↗ beta meanders › open-sided beta-meander › CPAP G-box domain › CPAP G-box domain 0.79 49.0 4.47e-01 80.2% 50.2%
3707357 77.2.1.1 ↗ beta meanders › open-sided beta-meander › Histone H3 K4-specific methyltransferase SET7/9-N › Histone H3 K4-specific methyltransferase SET7/9-N › MORN 0.78 49.0 4.49e-01 80.2% 51.1%
3718163 77.2.1.1 ↗ beta meanders › open-sided beta-meander › Histone H3 K4-specific methyltransferase SET7/9-N › Histone H3 K4-specific methyltransferase SET7/9-N › MORN 0.78 49.0 5.42e-01 80.2% 77.3%
4308299 77.3.1.3 ↗ beta meanders › open-sided beta-meander › CPAP G-box domain › CPAP G-box domain › MORN 0.77 50.0 5.62e-01 80.2% 82.1%
3707128 77.2.1.1 ↗ beta meanders › open-sided beta-meander › Histone H3 K4-specific methyltransferase SET7/9-N › Histone H3 K4-specific methyltransferase SET7/9-N › MORN 0.77 46.0 5.59e-01 80.2% 87.2%
3531694 77.2.1.1 ↗ beta meanders › open-sided beta-meander › Histone H3 K4-specific methyltransferase SET7/9-N › Histone H3 K4-specific methyltransferase SET7/9-N › MORN 0.76 50.0 4.30e-01 80.2% 45.8%
3407537 77.2.1.1 ↗ beta meanders › open-sided beta-meander › Histone H3 K4-specific methyltransferase SET7/9-N › Histone H3 K4-specific methyltransferase SET7/9-N › MORN 0.74 45.0 5.08e-01 80.2% 77.2%
3601199 77.2.1.0 ↗ beta meanders › open-sided beta-meander › Histone H3 K4-specific methyltransferase SET7/9-N › Histone H3 K4-specific methyltransferase SET7/9-N 0.71 44.0 5.51e-01 80.2% 95.8%
3598917 77.2.1.0 ↗ beta meanders › open-sided beta-meander › Histone H3 K4-specific methyltransferase SET7/9-N › Histone H3 K4-specific methyltransferase SET7/9-N 0.70 47.0 5.56e-01 80.2% 93.8%
3593136 77.2.1.0 ↗ beta meanders › open-sided beta-meander › Histone H3 K4-specific methyltransferase SET7/9-N › Histone H3 K4-specific methyltransferase SET7/9-N 0.65 49.0 5.04e-01 80.2% 80.6%
3965335 5084.1.1.1 ↗ beta barrels › Outer membrane meander beta-barrels › OMPA-like › OMPA-like › TbpB_B_D 0.57 40.0 3.74e-01 70.9% 70.7%
5033918 4252.1.1.0 ↗ beta barrels › AttH-like › AttH-like › AttH-like 0.54 37.0 3.79e-01 70.3% 91.1%
D2 medium residues 54-102
PDB
Domain cluster: rep: F-box_domain_protein__YP_009119184__Pandoravirus_inopinatum__1605721__D1-51
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF12937.13 best F-box-like 30.3 3.90e-07 93.9% 93.6%
D3 medium residues 334-385
PDB
Domain cluster: representative
CATH (16)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4r9iA01 3.30.497.10 Alpha Beta › 2-Layer Sandwich › Antithrombin; Chain I, domain 2 › Antithrombin, subunit I, domain 2 0.63 37.0 2.36e-01 90.4% 10.4%
1ut9A01 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.62 47.0 3.84e-01 82.7% 62.2%
2nwhA00 3.40.1190.20 Alpha Beta › 3-Layer(aba) Sandwich › UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase › Ribokinase 0.60 45.0 2.79e-01 80.8% 31.9%
8gjaD01 3.40.50.300 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases 0.58 40.0 2.58e-01 75.0% 87.0%
3payB02 2.60.40.2090 Mainly Beta › Sandwich › Immunoglobulin-like › 0.57 41.0 3.30e-01 86.5% 56.8%
6j9eJ00 3.30.160.560 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.56 43.0 3.99e-01 84.6% 71.2%
1cdcA00 2.60.40.10 Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins 0.55 40.0 3.40e-01 84.6% 43.8%
4akrA01 3.30.1140.60 Alpha Beta › 2-Layer Sandwich › Ribosomal protein S3 C-terminal domain › F-actin capping protein, alpha subunit 0.55 37.0 3.04e-01 82.7% 34.9%
2i0rA01 2.130.10.10 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase 0.55 42.0 2.60e-01 84.6% 34.0%
3icyA00 3.30.450.20 Alpha Beta › 2-Layer Sandwich › Beta-Lactamase › PAS domain 0.54 37.0 2.98e-01 75.0% 61.0%
6c6sD02 2.30.30.30 Mainly Beta › Roll › SH3 type barrels. › 0.52 41.0 4.07e-01 100.0% 91.7%
1tyeA00 2.130.10.130 Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › Integrin alpha, N-terminal 0.51 41.0 2.49e-01 98.1% 75.9%
1ta9B01 3.40.50.1970 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › 0.51 41.0 3.14e-01 98.1% 80.9%
8ornD01 2.50.20.10 Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › Lipoprotein localisation LolA/LolB/LppX 0.51 40.0 2.97e-01 96.2% 97.7%
3vskA01 3.90.1310.10 Alpha Beta › Alpha-Beta Complex › Penicillin-binding protein 2a (Domain 2) › Penicillin-binding protein 2a (Domain 2) 0.50 37.0 2.91e-01 82.7% 88.0%
6jwfA01 2.120.10.30 Mainly Beta › 6 Propeller › Neuraminidase › TolB, C-terminal domain 0.50 38.0 2.31e-01 84.6% 19.3%
ECOD (11)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3175567 3541.1.1.1 ↗ beta sandwiches › Atg29-Atg31 › Atg29-Atg31 › Atg29-Atg31 › ATG31 0.62 37.0 2.94e-01 80.8% 28.7%
3210917 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.60 47.0 4.01e-01 86.5% 61.2%
5080691 244.4.1.0 ↗ a+b two layers › FAD-linked reductases, C-terminal domain-like › Ni-Fe binding domain in nickel-iron hydrogenase large subunit › Ni-Fe binding domain in nickel-iron hydrogenase large subunit 0.60 45.0 3.55e-01 80.8% 89.8%
4193894 2.9.1.1 ↗ beta barrels › OB-fold › RNB domain-like › RNB domain-like › RNB 0.55 43.0 2.64e-01 90.4% 27.5%
3261013 63.1.1.0 ↗ beta barrels › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain › Mannose 6-phosphate receptor domain 0.54 39.0 3.02e-01 84.6% 34.5%
4142511 2.9.1.1 ↗ beta barrels › OB-fold › RNB domain-like › RNB domain-like › RNB 0.53 41.0 2.56e-01 90.4% 26.8%
3477512 11.1.1.179 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Ig_3 0.52 42.0 3.57e-01 98.1% 76.0%
4944757 375.1.1.0 ↗ few secondary structure elements › Rubredoxin-like › Rubredoxin-related › Rubredoxin-related 0.51 39.0 4.14e-01 82.7% 97.8%
3274536 11.1.1.29 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › TIG 0.51 40.0 3.39e-01 92.3% 79.0%
3994857 11.1.1.0 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like 0.50 36.0 3.61e-01 76.9% 89.1%
4239277 325.1.7.0 ↗ a+b complex topology › alpha/beta-Hammerhead/Barrel-sandwich hybrid › alpha/beta-Hammerhead/Barrel-sandwich hybrid › Single hybrid motif 0.50 43.0 3.54e-01 100.0% 62.0%
D4 medium residues 415-491_589-616
PDB
Domain cluster: representative
CATH (4)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4egxD01 6.10.250.2520 Special › Helix non-globular › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.75 25.0 3.18e-01 82.9% 47.8%
4cooA03 3.10.580.10 Alpha Beta › Roll › CBS-domain › CBS-domain 0.52 35.0 3.30e-01 70.5% 90.5%
3fhmA00 3.10.580.10 Alpha Beta › Roll › CBS-domain › CBS-domain 0.51 35.0 3.31e-01 71.4% 97.8%
6liuC02 3.90.1150.10 Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 › Aspartate Aminotransferase, domain 1 0.51 36.0 3.48e-01 72.4% 75.0%
ECOD (4)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4645764 71.1.1.3 ↗ beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › LolB 0.56 39.0 3.27e-01 70.5% 76.9%
4298074 71.1.1.3 ↗ beta meanders › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › Lipoprotein localization factors LolAB › LolB 0.55 38.0 3.16e-01 70.5% 74.9%
3338842 4291.1.1.1 ↗ beta barrels › Oxysterol-binding protein › Oxysterol-binding protein › Oxysterol-binding protein › Oxysterol_BP 0.53 45.0 3.14e-01 96.2% 75.5%
3908432 4291.1.1.1 ↗ beta barrels › Oxysterol-binding protein › Oxysterol-binding protein › Oxysterol-binding protein › Oxysterol_BP 0.52 45.0 3.09e-01 98.1% 72.2%
D5 medium residues 492-550_617-660
PDB
Domain cluster: rep: F-box_domain_containing_protein__YP_009483259__Pandoravirus_quercus__2107709__D363-500
CATH (9)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4obiA00 2.60.320.10 Mainly Beta › Sandwich › mini-chromosome maintenance (MCM) complex, domain 2 › N-utilization substance G protein NusG, insert domain 0.58 36.0 3.86e-01 97.1% 73.6%
3c6kA01 3.30.160.110 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › Sirohaem synthase, central domain 0.57 42.0 4.37e-01 94.2% 85.1%
1vmeB01 3.60.15.10 Alpha Beta › 4-Layer Sandwich › Metallo-beta-lactamase; Chain A › Ribonuclease Z/Hydroxyacylglutathione hydrolase-like 0.55 47.0 3.67e-01 100.0% 99.2%
2r55A00 3.30.530.20 Alpha Beta › 2-Layer Sandwich › Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 › START domain 0.54 40.0 3.26e-01 80.6% 61.1%
1e62A01 2.40.30.10 Mainly Beta › Beta Barrel › Elongation Factor Tu (Ef-tu); domain 3 › Translation factors 0.53 41.0 3.90e-01 84.5% 94.5%
3f6gA01 3.30.160.740 Alpha Beta › 2-Layer Sandwich › Double Stranded RNA Binding Domain › 0.53 30.0 3.64e-01 74.8% 96.6%
3itwA02 3.30.720.110 Alpha Beta › 2-Layer Sandwich › Signal recognition particle alu RNA binding heterodimer, srp9/1 › 0.53 23.0 2.92e-01 76.7% 67.9%
3ld7A00 2.60.320.10 Mainly Beta › Sandwich › mini-chromosome maintenance (MCM) complex, domain 2 › N-utilization substance G protein NusG, insert domain 0.53 33.0 3.57e-01 97.1% 74.7%
8jj7A01 3.40.50.1820 Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain 0.52 45.0 3.28e-01 99.0% 94.8%
ECOD (7)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
3941378 391.1.1.0 ↗ few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module 0.54 40.0 4.13e-01 88.3% 83.2%
3967405 211.1.1.1 ↗ a+b two layers › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase/Bleomycin resistance protein/Dihydroxybiphenyl dioxygenase › Glyoxalase 0.54 24.0 3.01e-01 75.7% 66.7%
5072132 331.10.2.0 ↗ a+b two layers › TBP-like › S-adenosylmethionine decarboxylase-related › Bacterial S-adenosylmethionine decarboxylase 0.53 35.0 3.80e-01 79.6% 86.3%
3455944 9.1.1.0 ↗ beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins 0.53 37.0 3.14e-01 71.8% 60.0%
4878467 271.1.1.1 ↗ beta barrels › GFP-like › GFP-like › GFP-like › GFP 0.52 28.0 2.92e-01 87.4% 54.2%
4471013 11.1.1.456 ↗ beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › YtkA 0.51 40.0 3.93e-01 86.4% 93.0%
3265830 241.6.1.1 ↗ a+b two layers › Type III secretory system chaperone-like › Arp2/3 complex subunits › Arp2/3 complex subunits › P34-Arc 0.50 37.0 3.59e-01 87.4% 69.6%