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major_capsid_protein

Euk-Vir

Spheniscid_alphaherpesvirus_1

major_capsid_protein__YP_009342387__Spheniscid_alphaherpesvirus_1__2560777

Identity

Accession:: YP_009342387 ↗
Protein ID:: major_capsid_protein
Kingdom:: euk

Quality

72.9 mean pLDDT

Taxonomy

Heunggongvirae› Peploviricota› Herviviricetes› Herpesvirales› Orthoherpesviridae› Mardivirus› Spheniscid_alphaherpesvirus_1

TaxID: 2560777

Cluster

View cluster (34 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 488-592

PDB

Domain cluster: rep: major_capsid_protein__YP_009046515__Falconid_herpesvirus_1__1510155__D483-586

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF03122.21 best	Herpes_MCP	47.1	1.20e-12	100.0%	6.3%

D2 medium residues 55-108_125-198

PDB

D3 medium residues 202-266

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF03122.21 best	Herpes_MCP	50.5	1.10e-13	100.0%	4.7%

CATH (5)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3aqbA00	1.20.120.1450	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) ›	0.62	46.0	3.69e-01	81.5%	74.8%
6orkA01	1.25.40.10	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain	0.58	39.0	2.70e-01	70.8%	45.7%
1ac5A00	3.40.50.1820	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Alpha/Beta hydrolase fold, catalytic domain	0.53	42.0	2.63e-01	98.5%	46.2%
8gj8A01	3.40.50.300	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › P-loop containing nucleotide triphosphate hydrolases	0.52	42.0	2.99e-01	100.0%	77.6%
5ux1D00	1.20.1260.10	Mainly Alpha › Up-down Bundle › Ferritin › Ferritin, core subunit, four-helix bundle	0.51	43.0	3.17e-01	98.5%	100.0%

ECOD (3)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3229793	198.1.1.0 ↗	alpha arrays › Saposin-like › Saposin-like › Saposin-like	0.66	47.0	4.37e-01	76.9%	72.9%
3305347	192.4.1.1 ↗	alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) › Ribosomal_L29	0.61	43.0	3.65e-01	81.5%	43.6%
None	—		0.53	43.0	3.01e-01	95.4%	71.2%

D4 medium residues 267-316_369-412

PDB

Domain cluster: rep: major_capsid_protein__NP_065524__Alcelaphine_gammaherpesvirus_1__35252__D265-300_361-395

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF03122.21 best	Herpes_MCP	44.0	1.00e-11	55.3%	3.7%
PF03122.21	Herpes_MCP	47.9	6.80e-13	48.9%	3.2%

D5 medium residues 413-487

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF03122.21 best	Herpes_MCP	64.4	7.10e-18	100.0%	5.2%

CATH (3)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3pijA01	2.115.10.20	Mainly Beta › 5 Propeller › Tachylectin-2; Chain A › Glycosyl hydrolase domain; family 43	0.51	38.0	2.53e-01	85.3%	71.1%
1f9qD00	2.40.50.40	Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) ›	0.50	27.0	2.88e-01	76.0%	51.5%
1mbyA00	2.40.50.930	Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) ›	0.50	28.0	2.82e-01	94.7%	49.3%

ECOD (6)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3283276	2484.1.1.1 ↗	mixed a+b and a/b › Ribonuclease H-like › Ribonuclease H-like › Ribonuclease H-like › HSP70	0.59	39.0	2.99e-01	100.0%	28.1%
3742835	5.1.5.1 ↗	beta duplicates or obligate multimers › beta-propeller-like › beta-propeller › 8-bladed › WD40	0.52	40.0	2.71e-01	89.3%	93.7%
3310306	1.1.1.20 ↗	beta barrels › cradle loop barrel › RIFT-related › acid protease › TAXi_C+TAXi_N	0.51	36.0	2.50e-01	76.0%	59.2%
4033043	616.1.1.41 ↗	alpha arrays › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › S15/NS1 RNA-binding domain › Terminase_4	0.51	30.0	2.87e-01	88.0%	47.8%
3223830	4.1.1.0 ↗	beta barrels › SH3 › SH3 › SH3	0.51	25.0	2.93e-01	84.0%	64.0%
3579053	327.5.1.2 ↗	a+b two layers › Alpha-lytic protease prodomain-like › a+b domain in acetyl-CoA synthetase-like proteins › a+b domain in acetyl-CoA synthetase-like proteins › AMP-binding_C	0.51	35.0	2.93e-01	72.0%	60.1%

D6 medium residues 621-727_818-917_950-963_1014-1040

PDB

Domain cluster: rep: protein_UL86__YP_004933858__Cynomolgus_macaque_cytomegalovirus_strain_Ottawa__944969__D580-722_767-802

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF03122.21 best	Herpes_MCP	83.2	1.50e-23	48.0%	7.6%
PF03122.21	Herpes_MCP	142.8	1.60e-41	43.1%	7.6%

CATH (1)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1td6A03	1.10.472.40	Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Hypothetical protein mg237 homolog; domain 3	0.57	18.0	2.94e-01	76.6%	73.9%

ECOD (4)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
7655	4066.1.1.1 ↗	a+b complex topology › Major capsid protein VP5 › Major capsid protein VP5 › Major capsid protein VP5 › Herpes_MCP	0.98	96.0	7.07e-01	100.0%	76.8%
2116543	4066.1.1.1 ↗	a+b complex topology › Major capsid protein VP5 › Major capsid protein VP5 › Major capsid protein VP5 › Herpes_MCP	0.84	81.0	6.29e-01	100.0%	83.8%
2738095	4066.1.1.1 ↗	a+b complex topology › Major capsid protein VP5 › Major capsid protein VP5 › Major capsid protein VP5 › Herpes_MCP	0.83	80.0	6.16e-01	100.0%	84.4%
3616362	109.46.1.1 ↗	alpha superhelices › Repetitive alpha hairpins › Helical domain in TOPLESS related protein 2 (TPR2) › Helical domain in TOPLESS related protein 2 (TPR2) › CTLH	0.51	22.0	2.87e-01	83.1%	67.1%

D7 medium residues 728-817

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF03122.21 best	Herpes_MCP	32.7	2.60e-08	100.0%	5.8%

ECOD (1)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
7655	4066.1.1.1 ↗	a+b complex topology › Major capsid protein VP5 › Major capsid protein VP5 › Major capsid protein VP5 › Herpes_MCP	0.90	85.0	5.04e-01	100.0%	16.4%

D8 medium residues 918-949_964-1013

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF03122.21 best	Herpes_MCP	27.4	1.00e-06	100.0%	7.2%

CATH (2)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
5jtwA06	6.20.50.160	Special › Other non-globular › N-terminal domain of TfIIb ›	0.60	27.0	3.03e-01	90.2%	51.6%
2a74A06	6.20.50.160	Special › Other non-globular › N-terminal domain of TfIIb ›	0.52	25.0	2.79e-01	90.2%	54.7%

ECOD (1)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3268976	868.1.1.0 ↗	a+b complex topology › mRNA triphosphatase CET1-related › mRNA triphosphatase CET1-related › mRNA triphosphatase CET1-related	0.60	33.0	2.58e-01	100.0%	23.5%

D9 medium residues 1200-1343

PDB

Domain cluster: rep: major_capsid_protein__NP_065524__Alcelaphine_gammaherpesvirus_1__35252__D1180-1286_1299-1321

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF03122.21 best	Herpes_MCP	222.0	1.90e-65	100.0%	10.8%