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capsid_protein

Euk-Vir

Xanthophyllomyces_dendrorhous_virus_L1A

capsid_protein__YP_007697650__Xanthophyllomyces_dendrorhous_virus_L1A__1167690

Identity

Accession:: YP_007697650 ↗
Protein ID:: capsid_protein
Kingdom:: euk

Quality

74.5 mean pLDDT

Taxonomy

Orthornavirae› Duplornaviricota› Chrymotiviricetes› Ghabrivirales› Orthototiviridae› Totivirus› Xanthophyllomyces_dendrorhous_virus_L1A

TaxID: 1167690

Cluster

View cluster (13 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 medium residues 33-48_448-609

PDB

Domain cluster: representative

CATH (4)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1m1cA00	3.90.1840.10	Alpha Beta › Alpha-Beta Complex › Major capsid protein › Major capsid protein	0.72	66.0	4.38e-01	96.6%	94.8%
4lsdF00	2.60.40.10	Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins	0.53	27.0	3.46e-01	80.9%	85.7%
8bxrA03	2.60.40.10	Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins	0.51	26.0	3.50e-01	79.8%	96.6%
2fhzA00	3.30.190.30	Alpha Beta › 2-Layer Sandwich › Ribulose 1,5 Bisphosphate Carboxylase/Oxygenase ›	0.50	30.0	3.81e-01	75.8%	99.1%

ECOD (9)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
7654	4065.1.1.1 ↗	a+b complex topology › L-A virus major coat protein-related › L-A virus major coat protein-related › L-A virus major coat protein-related › LA-virus_coat	0.72	66.0	4.38e-01	96.6%	94.8%
5057274	11.1.1.0 ↗	beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like	0.57	26.0	3.55e-01	79.8%	85.9%
4311589	11.1.1.0 ↗	beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like	0.53	25.0	3.37e-01	80.9%	87.1%
5047975	11.1.1.0 ↗	beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like	0.53	27.0	3.63e-01	80.9%	95.6%
3891682	11.1.1.21 ↗	beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Tissue_fac	0.52	27.0	3.41e-01	81.5%	85.0%
3231572	11.1.1.0 ↗	beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like	0.52	30.0	3.84e-01	73.6%	100.0%
4970102	11.1.4.0 ↗	beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Prealbumin-like	0.52	27.0	3.60e-01	70.2%	96.7%
5052420	11.1.1.0 ↗	beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like	0.51	26.0	3.47e-01	79.8%	93.3%
3494105	221.1.1.64 ↗	a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › Formin_GBD_N	0.50	23.0	3.36e-01	70.2%	96.2%

D2 medium residues 49-121

PDB

Domain cluster: representative

CATH (2)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1kx5A00	1.10.20.10	Mainly Alpha › Orthogonal Bundle › Histone, subunit A › Histone, subunit A	0.56	37.0	2.99e-01	72.6%	36.3%
4gakA00	3.10.129.10	Alpha Beta › Roll › Thiol Ester Dehydrase; Chain A › Hotdog Thioesterase	0.50	35.0	2.46e-01	72.6%	46.8%

ECOD (1)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3915805	524.1.1.1 ↗	alpha arrays › Ypt/Rab-GAP domain of gyp1p-like › Ypt/Rab-GAP domain of gyp1p › Ypt/Rab-GAP domain of gyp1p › RabGAP-TBC	0.52	38.0	2.92e-01	80.8%	77.4%

D3 medium residues 122-309

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF09220.17 best	LA-virus_coat	91.1	6.90e-26	100.0%	44.1%

CATH (2)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1m1cA00	3.90.1840.10	Alpha Beta › Alpha-Beta Complex › Major capsid protein › Major capsid protein	0.81	78.0	5.17e-01	100.0%	29.3%
2ychA02	3.30.1490.300	Alpha Beta › 2-Layer Sandwich › Dna Ligase; domain 1 ›	0.53	16.0	2.76e-01	94.1%	80.0%

ECOD (4)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
7654	4065.1.1.1 ↗	a+b complex topology › L-A virus major coat protein-related › L-A virus major coat protein-related › L-A virus major coat protein-related › LA-virus_coat	0.81	78.0	5.17e-01	100.0%	29.3%
4474711	3747.1.1.2 ↗	a+b two layers › Flagellar hook protein FlgE D0 domain › Flagellar hook protein FlgE D0 domain › Flagellar hook protein FlgE D0 domain › Flg_bb_rod,Flg_bbr_C	0.56	28.0	3.66e-01	87.8%	83.8%
3413150	4969.1.1.0 ↗	alpha bundles › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I › thumb domain in bacteriophage RB69-like DNA polymerase I	0.52	19.0	2.48e-01	94.7%	54.0%
4525882	3747.1.1.3 ↗	a+b two layers › Flagellar hook protein FlgE D0 domain › Flagellar hook protein FlgE D0 domain › Flagellar hook protein FlgE D0 domain › Flg_bbr_C	0.51	27.0	3.50e-01	87.2%	90.5%

D4 medium residues 310-447

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF09220.17 best	LA-virus_coat	61.8	5.60e-17	93.5%	27.6%

CATH (2)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4ye6A01	1.10.8.1290	Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Glutaminyl-tRNA synthetase, non-specific RNA binding region part 1, domain 1	0.55	26.0	3.02e-01	79.0%	58.7%
2wiyA00	1.10.630.10	Mainly Alpha › Orthogonal Bundle › Cytochrome p450 › Cytochrome P450	0.53	43.0	3.19e-01	87.7%	87.1%