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glycoprotein_B

Euk-Vir

Phascolarctid_gammaherpesvirus_1

glycoprotein_B__YP_010087456__Phascolarctid_gammaherpesvirus_1__2249313

Identity

Accession:: YP_010087456 ↗
Protein ID:: glycoprotein_B
Kingdom:: euk

Quality

71.3 mean pLDDT

Taxonomy

Heunggongvirae› Peploviricota› Herviviricetes› Herpesvirales› Orthoherpesviridae› Manticavirus› Phascolarctid_gammaherpesvirus_1

TaxID: 2249313

Cluster

View cluster (42 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 38-69_467-500

PDB

Domain cluster: rep: envelope_glycoprotein_B__YP_081514__Human_betaherpesvirus_5__10359__D76-104_527-554

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00606.24 best	Glycoprotein_B	48.6	1.00e-12	83.3%	17.6%

CATH (13)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3fvcA02	1.20.5.1890	Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces ›	0.79	55.0	4.75e-01	72.7%	100.0%
2gumA02	1.20.5.1890	Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces ›	0.78	54.0	4.67e-01	72.7%	100.0%
3mczA02	3.40.50.150	Alpha Beta › 3-Layer(aba) Sandwich › Rossmann fold › Vaccinia Virus protein VP39	0.57	40.0	2.76e-01	74.2%	74.0%
2di7A01	2.60.40.10	Mainly Beta › Sandwich › Immunoglobulin-like › Immunoglobulins	0.54	37.0	3.18e-01	71.2%	54.2%
1wihA00	3.30.1360.40	Alpha Beta › 2-Layer Sandwich › Gyrase A; domain 2 ›	0.54	39.0	3.63e-01	77.3%	63.1%
2o0bA01	3.65.10.10	Alpha Beta › Alpha-beta prism › UDP-n-acetylglucosamine1-carboxyvinyl-transferase; Chain › Enolpyruvate transferase domain	0.52	34.0	2.45e-01	71.2%	21.5%
2g1dA00	3.30.70.330	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain	0.52	38.0	3.38e-01	78.8%	71.4%
6lcqA00	3.30.30.10	Alpha Beta › 2-Layer Sandwich › Defensin A-like › Knottin, scorpion toxin-like	0.52	37.0	3.98e-01	75.8%	92.6%
6cl5A01	2.60.40.3940	Mainly Beta › Sandwich › Immunoglobulin-like ›	0.52	36.0	3.16e-01	74.2%	56.9%
2gqcA01	3.30.70.2080	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits ›	0.51	33.0	3.55e-01	77.3%	78.6%
3kdgA02	3.30.1370.100	Alpha Beta › 2-Layer Sandwich › Ribosomal Protein S8; Chain: A, domain 1 › MutL, C-terminal domain, regulatory subdomain	0.51	37.0	3.41e-01	84.8%	56.4%
4obuA01	3.90.1150.170	Alpha Beta › Alpha-Beta Complex › Aspartate Aminotransferase, domain 1 ›	0.51	42.0	2.99e-01	98.5%	78.2%
6u9hF02	3.30.70.1150	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › ACT-like. Chain A, domain 2	0.50	32.0	3.10e-01	75.8%	54.5%

ECOD (21)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2488247	4300.1.1.1 ↗	beta complex topology › Viral glycoprotein ectodomain-like › Viral glycoprotein ectodomain-like › Viral glycoprotein ectodomain-like › Glycoprotein_B	0.78	72.0	5.07e-01	100.0%	47.1%
3931130	4300.1.1.0 ↗	beta complex topology › Viral glycoprotein ectodomain-like › Viral glycoprotein ectodomain-like › Viral glycoprotein ectodomain-like	0.75	59.0	4.54e-01	86.4%	55.3%
3664860	387.1.5.15 ↗	few secondary structure elements › omega toxin-like › omega toxin-related › Scorpion toxin-like › SLR1-BP	0.58	39.0	4.38e-01	77.3%	92.0%
4162842	387.1.5.0 ↗	few secondary structure elements › omega toxin-like › omega toxin-related › Scorpion toxin-like	0.56	40.0	4.41e-01	77.3%	100.0%
4124687	304.162.1.1 ↗	a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain › CinA_KH	0.55	37.0	3.55e-01	72.7%	60.0%
4322692	304.162.1.1 ↗	a+b two layers › Alpha-beta plaits › Competence or damage-inducible protein CinA middle domain › Competence or damage-inducible protein CinA middle domain › CinA_KH	0.55	37.0	3.49e-01	72.7%	56.2%
4022173	320.1.1.0 ↗	a+b two layers › R3H domain-like › R3H domain › R3H domain	0.54	37.0	3.74e-01	71.2%	72.3%
3268478	3122.1.1.0 ↗	a+b complex topology › MESD › MESD › MESD	0.53	40.0	3.69e-01	80.3%	67.1%
3709828	3016.1.1.3 ↗	a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › Aminotran_5	0.53	44.0	2.72e-01	97.0%	76.8%
4509594	304.28.1.2 ↗	a+b two layers › Alpha-beta plaits › Ferredoxin domains in multidrug efflux transporter › Multidrug efflux transporter AcrB pore domain › Sec_GG	0.53	38.0	3.53e-01	75.8%	61.2%
2831815	101.1.2.47 ↗	alpha arrays › HTH › HTH › winged helix domain › S10_plectin	0.53	36.0	3.41e-01	71.2%	66.7%
3286797	304.154.1.0 ↗	a+b two layers › Alpha-beta plaits › Regulator of polyketide synthase expression N-terminal domain › Regulator of polyketide synthase expression N-terminal domain	0.53	37.0	2.87e-01	75.8%	52.3%
3691787	3016.1.1.0 ↗	a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases	0.52	36.0	2.82e-01	72.7%	40.7%
3597807	3016.1.1.0 ↗	a+b two layers › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases › C-terminal domain in some PLP-dependent transferases	0.52	37.0	3.08e-01	80.3%	39.2%
2604944	387.1.5.1 ↗	few secondary structure elements › omega toxin-like › omega toxin-related › Scorpion toxin-like › Gamma-thionin	0.52	37.0	3.98e-01	75.8%	92.6%
3233775	304.20.1.3 ↗	a+b two layers › Alpha-beta plaits › PAP/Archaeal CCA-adding enzyme, C-terminal domain › PAP/Archaeal CCA-adding enzyme, C-terminal domain › Nrap_D6	0.52	36.0	2.98e-01	75.8%	63.1%
3445190	387.1.5.1 ↗	few secondary structure elements › omega toxin-like › omega toxin-related › Scorpion toxin-like › Gamma-thionin	0.51	36.0	4.01e-01	77.3%	100.0%
3971738	304.8.1.102 ↗	a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT_3, ACT_7	0.51	37.0	2.98e-01	75.8%	71.9%
3698115	304.8.1.10 ↗	a+b two layers › Alpha-beta plaits › ACT-like › ACT-like › ACT_7	0.51	36.0	2.74e-01	75.8%	81.2%
4621064	305.2.1.1 ↗	a+b two layers › DCoH-like › Pterin-4a-carbinolamine dehydratase (PCD)/dimerization cofactor of HNF1 (DCoH) › Pterin-4a-carbinolamine dehydratase (PCD)/dimerization cofactor of HNF1 (DCoH) › Pterin_4a	0.51	35.0	3.20e-01	72.7%	54.4%
5056043	304.120.1.0 ↗	a+b two layers › Alpha-beta plaits › Ferredoxin-like domain in ThiI › Ferredoxin-like domain in ThiI	0.51	34.0	3.46e-01	75.8%	70.8%

D2 medium residues 89-126_163-176_199-236

PDB

Domain cluster: representative

Pfam (2)

Accession	Name	Score	E-value	Q cov	HMM cov
PF17416.9 best	Glycoprot_B_PH1	32.9	7.40e-08	53.3%	20.5%
PF17416.9	Glycoprot_B_PH1	63.1	4.10e-17	53.3%	18.6%

CATH (4)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3lhnA00	2.40.128.640	Mainly Beta › Beta Barrel › Lipocalin ›	0.77	41.0	3.85e-01	95.6%	43.9%
4n1vA00	4.10.520.10	Few Secondary Structures › Irregular › HU Protein; Chain A › IHF-like DNA-binding proteins	0.62	29.0	2.92e-01	78.9%	39.8%
6qdwt00	3.30.70.330	Alpha Beta › 2-Layer Sandwich › Alpha-Beta Plaits › RRM (RNA recognition motif) domain	0.55	25.0	2.55e-01	76.7%	35.5%
1f8vC00	2.60.120.20	Mainly Beta › Sandwich › Jelly Rolls ›	0.50	44.0	3.06e-01	97.8%	79.7%

ECOD (7)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2530507	220.3.1.3 ↗	beta barrels › PH domain-like › first barrel domain in viral glycoproteins › first barrel domain in viral glycoproteins › Glycoprot_B_PH1	0.90	85.0	6.14e-01	100.0%	66.4%
1688016	220.3.1.3 ↗	beta barrels › PH domain-like › first barrel domain in viral glycoproteins › first barrel domain in viral glycoproteins › Glycoprot_B_PH1	0.90	85.0	6.25e-01	100.0%	68.8%
3484264	382.1.1.0 ↗	few secondary structure elements › Snake toxin-like › Snake toxin-like › Snake toxin-like	0.54	37.0	3.97e-01	80.0%	81.2%
5075107	324.1.1.1 ↗	a+b two layers › OsmC-like › OsmC-like › OsmC-like › OsmC	0.53	28.0	2.47e-01	87.8%	32.1%
3408652	11.1.1.0 ↗	beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like	0.52	38.0	3.13e-01	80.0%	43.1%
3411669	11.1.1.0 ↗	beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like	0.51	37.0	3.52e-01	81.1%	62.7%
5074083	11.1.1.91 ↗	beta sandwiches › Immunoglobulin-like beta-sandwich › Immunoglobulin-related › Immunoglobulin/Fibronectin type III/E set domains/PapD-like › Spo0M	0.50	40.0	3.43e-01	86.7%	57.2%

D3 medium residues 390-400_424-466

PDB

D4 medium residues 501-591

PDB

Domain cluster: rep: envelope_glycoprotein_B__YP_009342376__Spheniscid_alphaherpesvirus_1__2560777__D566-653

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00606.24 best	Glycoprotein_B	105.8	3.30e-30	100.0%	41.0%