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major_capsid_protein

Euk-Vir

Human_betaherpesvirus_6B

major_capsid_protein__NP_050238__Human_betaherpesvirus_6B__32604

Identity

Accession:: NP_050238 ↗
Protein ID:: major_capsid_protein
Kingdom:: euk

Quality

71.6 mean pLDDT

Taxonomy

Heunggongvirae› Peploviricota› Herviviricetes› Herpesvirales› Orthoherpesviridae› Roseolovirus› Human_betaherpesvirus_6B

TaxID: 32604

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 medium residues 18-98_114-184

PDB

D2 medium residues 206-311_354-388_1022-1030_1065-1080

PDB

Domain cluster: rep: major_capsid_protein__YP_002333524__Equid_alphaherpesvirus_9__55744__D231-307_358-408_1051-1122

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF03122.21 best	Herpes_MCP	100.7	7.90e-29	65.7%	7.7%
PF03122.21	Herpes_MCP	27.9	7.50e-07	27.1%	2.7%

CATH (4)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2pk8A00	3.30.2320.10	Alpha Beta › 2-Layer Sandwich › hypothetical protein PF0899 fold › hypothetical protein PF0899 domain	0.67	39.0	5.03e-01	81.3%	100.0%
6xgpB01	3.30.1930.10	Alpha Beta › 2-Layer Sandwich › capsid protein of prophage fold › capsid protein of prophage domain	0.63	49.0	5.44e-01	88.0%	99.3%
3k7cA00	3.10.450.50	Alpha Beta › Roll › Nuclear Transport Factor 2; Chain: A, ›	0.58	22.0	2.72e-01	97.0%	52.8%
1b3qA04	2.40.50.180	Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › CheA-289, Domain 4	0.55	22.0	3.60e-01	73.5%	100.0%

ECOD (5)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4036496	298.4.1.1 ↗	a+b two layers › FwdE/GAPDH domain-like › V-type ATPase subunit E › V-type ATPase subunit E › vATP-synt_E	0.67	33.0	3.72e-01	84.3%	59.4%
4638799	298.4.1.0 ↗	a+b two layers › FwdE/GAPDH domain-like › V-type ATPase subunit E › V-type ATPase subunit E	0.61	34.0	3.86e-01	84.9%	70.4%
4070529	298.4.1.1 ↗	a+b two layers › FwdE/GAPDH domain-like › V-type ATPase subunit E › V-type ATPase subunit E › vATP-synt_E	0.61	32.0	3.33e-01	83.7%	51.9%
5081487	2485.3.1.10 ↗	a+b three layers › Thioredoxin-like › Major capsid protein gp5 › Major capsid protein gp5 › DUF5309	0.56	47.0	3.98e-01	89.8%	59.7%
3471200	11.1.1.0 ↗	beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like	0.53	29.0	3.73e-01	88.0%	92.6%

D3 medium residues 389-450_1004-1021_1081-1128_1145-1167

PDB

Domain cluster: representative

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF03122.21 best	Herpes_MCP	63.7	1.10e-17	48.3%	6.3%
PF03122.21	Herpes_MCP	63.8	1.10e-17	41.7%	4.5%

CATH (1)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3oyyA02	2.40.50.140	Mainly Beta › Beta Barrel › OB fold (Dihydrolipoamide Acetyltransferase, E2P) › Nucleic acid-binding proteins	0.52	24.0	3.48e-01	90.7%	100.0%

ECOD (1)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
4113537	2.1.1.327 ↗	beta barrels › OB-fold › Nucleic acid-binding protein › Nucleic acid-binding protein › PF27401	0.51	23.0	3.46e-01	89.4%	100.0%

D4 medium residues 451-479_505-566

PDB

Domain cluster: rep: Cy118__YP_009337526__Cynomolgus_cytomegalovirus__1919083__D473-550

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF03122.21 best	Herpes_MCP	64.6	6.30e-18	100.0%	4.7%

CATH (6)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
1s7mA03	2.20.25.140	Mainly Beta › Single Sheet › N-terminal domain of TfIIb ›	0.69	25.0	3.93e-01	70.3%	100.0%
2v8qB00	6.20.250.60	Special › Other non-globular › Double Stranded RNA Binding Domain ›	0.58	30.0	3.36e-01	76.9%	61.6%
2ci8A01	3.30.505.10	Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain	0.57	32.0	3.82e-01	82.4%	87.5%
3pieC05	2.170.260.40	Mainly Beta › Beta Complex › paz domain ›	0.56	38.0	3.16e-01	91.2%	38.9%
2oq1A03	3.30.505.10	Alpha Beta › 2-Layer Sandwich › SHC Adaptor Protein › SH2 domain	0.51	36.0	3.57e-01	90.1%	68.0%
1v7pB00	3.10.100.10	Alpha Beta › Roll › Mannose-Binding Protein A; Chain A › Mannose-Binding Protein A, subunit A	0.50	35.0	3.20e-01	73.6%	85.8%

ECOD (15)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3623534	220.1.1.0 ↗	beta barrels › PH domain-like › PH domain-like › PH domain-like	0.63	31.0	3.19e-01	71.4%	45.6%
3892942	391.1.2.0 ↗	few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › VWC domain-related	0.62	32.0	4.08e-01	78.0%	90.0%
3624010	391.1.1.0 ↗	few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module	0.60	31.0	3.82e-01	86.8%	86.0%
3584990	391.1.1.0 ↗	few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module	0.56	29.0	3.75e-01	85.7%	97.7%
3576281	391.1.2.1 ↗	few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › VWC domain-related › VWC	0.56	34.0	3.94e-01	87.9%	84.6%
3996530	391.1.2.0 ↗	few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › VWC domain-related	0.55	33.0	3.84e-01	89.0%	84.6%
4530301	7.1.1.10 ↗	beta barrels › PDZ domain › PDZ domain › PDZ domain › PDZ_6	0.55	31.0	3.28e-01	73.6%	60.0%
4003074	391.1.2.0 ↗	few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › VWC domain-related	0.55	28.0	3.61e-01	85.7%	100.0%
3403126	394.1.1.1 ↗	few secondary structure elements › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › CBM_14	0.54	37.0	3.25e-01	90.1%	46.8%
4178004	274.1.1.1 ↗	a+b two layers › Pili subunits › Pili subunits › Pili subunits › Pilin	0.54	43.0	4.02e-01	90.1%	91.7%
3403146	394.1.1.1 ↗	few secondary structure elements › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › CBM_14	0.54	38.0	4.21e-01	91.2%	98.5%
3528425	209.1.1.1 ↗	a+b complex topology › C-type lectin-like › C-type lectin-like › C-type lectin-like › Lectin_C	0.51	36.0	3.38e-01	73.6%	91.3%
4266074	394.1.1.1 ↗	few secondary structure elements › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › Invertebrate chitin-binding proteins › CBM_14	0.51	33.0	3.81e-01	86.8%	100.0%
4003988	391.1.1.7 ↗	few secondary structure elements › Fibronectin type I module-like › Fibronectin type I module-like › Fibronectin type I module › Fn1_2	0.50	32.0	3.47e-01	73.6%	77.3%
5045308	223.1.1.0 ↗	a+b three layers › Profilin-like › sensor domains › sensor domains	0.50	41.0	3.35e-01	95.6%	46.1%

D5 medium residues 605-715_835-849

PDB

Domain cluster: rep: protein_UL86__YP_004933858__Cynomolgus_macaque_cytomegalovirus_strain_Ottawa__944969__D580-722_767-802

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF03122.21 best	Herpes_MCP	129.9	1.20e-37	88.9%	8.3%

CATH (3)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3iieB03	1.10.1740.10	Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif	0.55	22.0	2.64e-01	74.6%	49.4%
5a4uF02	1.20.1050.10	Mainly Alpha › Up-down Bundle › Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2 ›	0.55	43.0	4.38e-01	83.3%	90.1%
2or0B01	1.10.540.10	Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain	0.54	43.0	4.40e-01	84.9%	98.4%

ECOD (8)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2116543	4066.1.1.1 ↗	a+b complex topology › Major capsid protein VP5 › Major capsid protein VP5 › Major capsid protein VP5 › Herpes_MCP	0.93	89.0	5.74e-01	100.0%	52.8%
2738095	4066.1.1.1 ↗	a+b complex topology › Major capsid protein VP5 › Major capsid protein VP5 › Major capsid protein VP5 › Herpes_MCP	0.81	75.0	4.89e-01	100.0%	53.5%
5015299	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.59	48.0	3.11e-01	88.1%	30.4%
3703546	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.57	40.0	3.45e-01	73.8%	56.6%
3614324	109.1.1.52 ↗	alpha superhelices › Repetitive alpha hairpins › Glutathione S-transferase (GST)-C › Glutathione S-transferase (GST)-C › PF26179	0.54	42.0	3.94e-01	84.9%	100.0%
4991313	5050.1.1.1 ↗	alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Sugar_tr	0.52	38.0	3.18e-01	77.0%	99.1%
3592091	603.2.1.27 ↗	alpha bundles › STAT-like › STAT › STAT › PF26179	0.52	39.0	3.70e-01	82.5%	99.4%
3274466	109.4.1.0 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat	0.51	40.0	3.39e-01	85.7%	80.9%

D6 medium residues 716-726_877-887_900-1003

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF03122.21 best	Herpes_MCP	115.8	2.20e-33	86.5%	7.1%

ECOD (1)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2116543	4066.1.1.1 ↗	a+b complex topology › Major capsid protein VP5 › Major capsid protein VP5 › Major capsid protein VP5 › Herpes_MCP	0.95	92.0	5.90e-01	100.0%	60.7%

D7 medium residues 1168-1295

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	187.8	4.10e-55	100.0%	9.4%