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F-box_domain_containing_protein

Euk-Vir

Pandoravirus_neocaledonia

F-box_domain_containing_protein__YP_009482248__Pandoravirus_neocaledonia__2107708

Identity

Accession:: YP_009482248 ↗
Protein ID:: F-box_domain_containing_protein
Kingdom:: euk

Quality

77.4 mean pLDDT

Taxonomy

Pandoravirus› Pandoravirus_neocaledonia

TaxID: 2107708

Cluster

View cluster (16 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 73-179

PDB

Domain cluster: representative

CATH (9)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1xffA00	3.60.20.10	Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain	0.57	45.0	3.51e-01	85.0%	76.9%
2z15A00	3.90.640.90	Alpha Beta › Alpha-Beta Complex › Actin; Chain A, domain 4 › Anti-proliferative protein, N-terminal domain	0.57	39.0	3.80e-01	70.1%	93.3%
2fpnA02	3.30.360.40	Alpha Beta › 2-Layer Sandwich › Dihydrodipicolinate Reductase; domain 2 › YwmB-like	0.56	31.0	3.85e-01	76.6%	89.2%
2byoA00	2.50.20.20	Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A ›	0.55	42.0	3.54e-01	82.2%	79.2%
1iwmA00	2.50.20.10	Mainly Beta › Clam › outer membrane lipoprotein receptor (LolB), chain A › Lipoprotein localisation LolA/LolB/LppX	0.52	42.0	3.55e-01	86.0%	79.1%
3cxbA01	3.30.2440.10	Alpha Beta › 2-Layer Sandwich › Secreted effector protein SifA fold › Secreted effector protein SifA	0.51	41.0	4.06e-01	86.9%	98.3%
4zfjD00	3.60.20.10	Alpha Beta › 4-Layer Sandwich › Glutamine Phosphoribosylpyrophosphate, subunit 1, domain 1 › Aminohydrolase, N-terminal nucleophile (Ntn) domain	0.51	44.0	3.52e-01	97.2%	82.8%
1k32A01	2.120.10.60	Mainly Beta › 6 Propeller › Neuraminidase › Tricorn protease N-terminal domain	0.51	44.0	3.36e-01	98.1%	85.7%
3ei3A02	2.130.10.10	Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase	0.50	40.0	2.94e-01	89.7%	91.1%

ECOD (10)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4275209	4237.1.1.1 ↗	beta barrels › FomD-like › FomD-like › FomD-like › DUF402	0.58	42.0	3.49e-01	73.8%	46.7%
3965967	243.3.1.0 ↗	a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin	0.58	34.0	3.51e-01	76.6%	60.0%
3617898	79.1.1.0 ↗	beta duplicates or obligate multimers › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain	0.57	47.0	4.18e-01	86.0%	69.7%
3224985	4072.1.1.0 ↗	a+b complex topology › BTG domain-like › BTG domain-like › BTG domain-like	0.57	39.0	3.94e-01	72.0%	95.5%
3619569	4072.1.1.1 ↗	a+b complex topology › BTG domain-like › BTG domain-like › BTG domain-like › BTG	0.57	39.0	3.65e-01	70.1%	89.2%
5049973	223.2.1.0 ↗	a+b three layers › Profilin-like › profilin-like › profilin-like	0.54	43.0	4.01e-01	87.9%	95.7%
4975431	331.3.1.0 ↗	a+b two layers › TBP-like › Bet v1-like › Bet v1-like	0.54	37.0	3.98e-01	71.0%	94.4%
342906	10.1.1.27 ↗	beta sandwiches › jelly-roll › Concanavalin A-like › Concanavalin A-like lectins/glucanases › Alginate_lyase2	0.52	40.0	3.17e-01	82.2%	44.3%
185328	241.13.1.1 ↗	a+b two layers › Type III secretory system chaperone-like › N-terminal domain of secreted effector protein sifA › N-terminal domain of secreted effector protein sifA › Sif	0.51	41.0	4.08e-01	86.9%	98.3%
4988847	243.3.1.0 ↗	a+b two layers › Cystatin-like › Cystatin/monellin › Cystatin/monellin	0.51	31.0	3.57e-01	76.6%	86.7%

D2 medium residues 180-301

PDB

Domain cluster: representative

CATH (13)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2af5A02	3.90.930.1	Alpha Beta › Alpha-Beta Complex › Outer Surface Protein A; domain 3 ›	0.66	50.0	4.77e-01	100.0%	69.6%
3g7gH00	2.40.160.20	Mainly Beta › Beta Barrel › Porin ›	0.63	54.0	5.03e-01	92.6%	88.8%
2x9oA00	3.40.1500.20	Alpha Beta › 3-Layer(aba) Sandwich › oxygen-dependent coproporphyrinogen oxidase ›	0.57	49.0	3.98e-01	94.3%	89.3%
2bjfA01	3.60.60.10	Alpha Beta › 4-Layer Sandwich › Penicillin V Acylase; Chain A › Penicillin V Acylase; Chain A	0.56	46.0	3.39e-01	87.7%	81.1%
1ospO01	2.40.128.160	Mainly Beta › Beta Barrel › Lipocalin › C1 set domains (antibody constant domain-like)	0.56	43.0	4.63e-01	83.6%	99.0%
7szeB02	3.90.380.10	Alpha Beta › Alpha-Beta Complex › Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1 › Naphthalene 1,2-dioxygenase Alpha Subunit; Chain A, domain 1	0.54	45.0	3.89e-01	88.5%	64.7%
3hdjA01	3.30.1780.10	Alpha Beta › 2-Layer Sandwich › ornithine cyclodeaminase, domain 1 › ornithine cyclodeaminase, domain 1	0.53	44.0	4.23e-01	95.9%	76.4%
1o7dD01	2.70.98.30	Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Golgi alpha-mannosidase II; domain 4	0.53	42.0	3.31e-01	85.2%	94.3%
4h5iB00	2.130.10.10	Mainly Beta › 7 Propeller › Methylamine Dehydrogenase; Chain H › YVTN repeat-like/Quinoprotein amine dehydrogenase	0.52	44.0	3.27e-01	94.3%	88.1%
1pu4A03	2.70.98.20	Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Copper amine oxidase, catalytic domain	0.52	47.0	3.27e-01	98.4%	88.5%
3sc7X01	2.115.10.20	Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43	0.52	42.0	3.15e-01	90.2%	55.7%
1a2vA03	2.70.98.20	Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Copper amine oxidase, catalytic domain	0.51	42.0	2.95e-01	93.4%	90.9%
1av4A03	2.70.98.20	Mainly Beta › Distorted Sandwich › Beta-galactosidase; Chain A, domain 5 › Copper amine oxidase, catalytic domain	0.50	45.0	3.09e-01	98.4%	85.4%

ECOD (21)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3231343	77.1.1.10 ↗	beta meanders › open-sided beta-meander › Outer surface protein › Outer surface protein › PF28998	0.81	50.0	4.88e-01	83.6%	57.7%
4107854	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	0.71	51.0	5.55e-01	87.7%	86.7%
3601903	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	53.0	4.77e-01	100.0%	58.7%
3890448	77.3.1.3 ↗	beta meanders › open-sided beta-meander › CPAP G-box domain › CPAP G-box domain › MORN	0.70	55.0	5.54e-01	99.2%	82.5%
4334199	77.1.1.1 ↗	beta meanders › open-sided beta-meander › Outer surface protein › Outer surface protein › Lipoprotein_1	0.70	47.0	4.74e-01	81.1%	67.2%
3844285	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	0.70	55.0	5.02e-01	100.0%	64.5%
3422547	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	0.69	52.0	5.15e-01	100.0%	75.2%
1099835	77.1.1.1 ↗	beta meanders › open-sided beta-meander › Outer surface protein › Outer surface protein › Lipoprotein_1	0.67	49.0	5.21e-01	100.0%	86.8%
4583801	77.1.1.1 ↗	beta meanders › open-sided beta-meander › Outer surface protein › Outer surface protein › Lipoprotein_1	0.65	58.0	4.54e-01	100.0%	47.3%
2649512	77.1.1.1 ↗	beta meanders › open-sided beta-meander › Outer surface protein › Outer surface protein › Lipoprotein_1	0.63	48.0	4.13e-01	98.4%	51.9%
4008697	5084.5.1.22 ↗	beta barrels › Outer membrane meander beta-barrels › Porins › Porin › DUF3971	0.61	55.0	4.00e-01	98.4%	42.1%
3246316	9.1.1.12 ↗	beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins › THAP4_heme-bd	0.59	53.0	4.57e-01	100.0%	90.7%
5044087	3504.3.1.1 ↗	beta barrels › MutM N-terminal domain-like › Fibrinogen binding protein N-terminal domain › Fibrinogen binding protein N-terminal domain › NFACT_N	0.58	49.0	4.56e-01	89.3%	95.3%
3643596	77.1.1.0 ↗	beta meanders › open-sided beta-meander › Outer surface protein › Outer surface protein	0.57	48.0	4.57e-01	100.0%	77.9%
3399293	79.1.1.23 ↗	beta duplicates or obligate multimers › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain › Phage tail fiber protein trimerization domain › Chitin_bind_4	0.56	41.0	4.44e-01	95.1%	89.3%
4341629	12.3.1.29 ↗	beta sandwiches › Glycosyl hydrolase domain-like › supersandwich › supersandwich › Gal_mutarotas_3	0.55	41.0	3.18e-01	77.9%	97.0%
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	0.54	50.0	4.94e-01	100.0%	95.4%
3610069	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	0.54	48.0	3.96e-01	100.0%	54.4%
4199183	9.1.1.0 ↗	beta barrels › Lipocalins/Streptavidin › Lipocalins › Lipocalins	0.54	47.0	4.50e-01	95.9%	88.3%
3642414	5.3.1.1 ↗	beta duplicates or obligate multimers › beta-propeller-like › beta-Prism II › beta-Prism II › S_locus_glycop	0.51	36.0	3.40e-01	72.1%	100.0%
3618224	5.1.4.1 ↗	beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 7-bladed › WD40	0.50	43.0	3.24e-01	98.4%	68.4%

D3 medium residues 302-356

PDB

Domain cluster: representative

CATH (15)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
5jxxA02	1.20.1180.10	Mainly Alpha › Up-down Bundle › Udp N-acetylglucosamine O-acyltransferase; Domain 2 › Udp N-acetylglucosamine O-acyltransferase, C-terminal domain	0.60	42.0	3.99e-01	72.7%	80.3%
3ooqA02	3.20.20.140	Alpha Beta › Alpha-Beta Barrel › TIM Barrel › Metal-dependent hydrolases	0.59	42.0	2.69e-01	76.4%	35.7%
1jr8A00	1.20.120.310	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › ERV/ALR sulfhydryl oxidase domain	0.59	47.0	3.93e-01	94.5%	82.9%
1uujA00	1.20.960.30	Mainly Alpha › Up-down Bundle › Mitochondrial Import Receptor Subunit Tom20; Chain A ›	0.58	43.0	3.92e-01	83.6%	59.2%
1lp1A00	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	0.57	37.0	3.80e-01	100.0%	69.1%
2b8iA00	1.20.1280.100	Mainly Alpha › Up-down Bundle › Monooxygenase › Pas factor, saposin domain	0.57	45.0	4.24e-01	100.0%	98.7%
7ovuA01	3.40.630.30	Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT)	0.55	44.0	3.15e-01	98.2%	26.9%
1cukA03	1.10.8.10	Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain	0.55	33.0	3.48e-01	80.0%	66.7%
1e7lA02	1.10.720.10	Mainly Alpha › Orthogonal Bundle › Transcription Termination Factor Rho, Rna-binding Domain; Chain A, Domain 1 ›	0.55	46.0	4.61e-01	100.0%	96.4%
2v57A00	1.10.357.10	Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2	0.53	42.0	3.02e-01	90.9%	46.2%
2r1iA01	3.40.630.30	Alpha Beta › 3-Layer(aba) Sandwich › Aminopeptidase › Gcn5-related N-acetyltransferase (GNAT)	0.53	40.0	3.15e-01	100.0%	36.9%
2dzlA00	1.10.8.10	Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Ubiquitin-associated (UBA) domain	0.52	33.0	3.22e-01	100.0%	54.5%
2rn7A01	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	35.0	3.38e-01	74.5%	68.2%
1oqcA00	1.20.120.310	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › ERV/ALR sulfhydryl oxidase domain	0.50	36.0	3.12e-01	85.5%	91.1%
5z4zC00	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	0.50	41.0	3.65e-01	100.0%	73.9%

ECOD (12)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3250088	101.46.1.1 ↗	alpha arrays › HTH › Parafibromin N-terminal domain › Parafibromin N-terminal domain › CDC73_N	0.60	45.0	3.75e-01	80.0%	77.9%
4471327	3455.1.1.0 ↗	alpha arrays › WY-domain in RXLR effectors › WY-domain in RXLR effectors › WY-domain in RXLR effectors	0.58	41.0	4.17e-01	83.6%	78.2%
3684914	101.1.1.354 ↗	alpha arrays › HTH › HTH › Three-helical HTH › DUF7626	0.57	40.0	4.08e-01	74.5%	83.6%
4273807	314.1.1.0 ↗	a+b three layers › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases › Class II aaRS and biotin synthetases	0.57	42.0	2.54e-01	83.6%	78.6%
5046694	101.1.2.0 ↗	alpha arrays › HTH › HTH › winged helix domain	0.56	39.0	3.91e-01	94.5%	72.7%
5042947	101.35.1.0 ↗	alpha arrays › HTH › DNA repair regulatory protein RecX › DNA repair regulatory protein RecX	0.56	36.0	3.81e-01	96.4%	74.0%
None	—		0.54	45.0	3.15e-01	98.2%	28.7%
4926838	101.43.1.0 ↗	alpha arrays › HTH › Phage G20C small terminase N-terminal domain › Phage G20C small terminase N-terminal domain	0.54	36.0	3.48e-01	70.9%	66.2%
3735546	213.1.1.25 ↗	a+b three layers › Nat/Ivy › Acyl-CoA N-acyltransferases (Nat) › Acyl-CoA N-acyltransferases (Nat) › Acetyltransf_3	0.53	41.0	2.84e-01	98.2%	21.3%
4231284	192.7.1.2 ↗	alpha bundles › Long alpha-hairpin › tRNA-binding arm › tRNA-binding arm › Seryl_tRNA_N	0.52	39.0	3.19e-01	83.6%	96.4%
3297949	592.7.1.2 ↗	alpha arrays › PWI domain-like › GIPC1 GH2 domain › GIPC1 GH2 domain › PWI	0.51	36.0	3.52e-01	78.2%	73.8%
3300095	592.1.1.1 ↗	alpha arrays › PWI domain-like › PWI domain › PWI domain › PWI	0.51	36.0	3.50e-01	78.2%	73.8%