←Back to structures

gag_protein

Euk-Vir

Simian_retrovirus_8

gag_protein__YP_009305199__Simian_retrovirus_8__1904439

Identity

Accession:: YP_009305199 ↗
Protein ID:: gag_protein
Kingdom:: euk

Quality

62.4 mean pLDDT

Taxonomy

Pararnavirae› Artverviricota› Revtraviricetes› Ortervirales› Retroviridae› Betaretrovirus› Simian_retrovirus_8

TaxID: 1904439

Cluster

View cluster (4 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 7-111

PDB

Domain cluster: rep: putative_group-specific_antigen__YP_009243639__Bovine_retrovirus_CH15__1822365__D9-108

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF02337.23 best	Gag_p10	91.0	5.30e-26	81.0%	98.8%

D2 medium residues 302-440

PDB

Domain cluster: representative

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF00607.26 best	Gag_p24	155.9	6.70e-46	89.2%	97.7%

CATH (17)

Domain ID	Class ID	Classification	TM-score	Bits	E-value	Q cov	T cov
2kgfA00	1.10.375.10	Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein	0.90	85.0	8.57e-01	99.3%	98.6%
1l6nA02	1.10.375.10	Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein	0.78	65.0	6.69e-01	87.1%	99.2%
2xgvA00	1.10.375.10	Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein	0.78	70.0	7.13e-01	99.3%	100.0%
2xguB00	1.10.375.10	Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein	0.77	69.0	7.10e-01	99.3%	100.0%
1d1dA01	1.10.375.10	Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein	0.76	71.0	7.12e-01	100.0%	97.9%
1u7kA00	1.10.375.10	Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein	0.74	65.0	6.73e-01	98.6%	100.0%
1eiaA01	1.10.375.10	Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein	0.72	64.0	6.58e-01	100.0%	99.2%
1p65A00	6.10.140.90	Special › Helix non-globular › Helix Hairpins ›	0.65	24.0	3.75e-01	82.7%	84.2%
2a0uB01	1.20.120.420	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › translation initiation factor eif-2b, domain 1	0.56	42.0	4.03e-01	86.3%	68.1%
4nqfA00	1.20.120.330	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleotidyltransferases domain 2	0.54	40.0	4.04e-01	78.4%	93.8%
4crwA00	1.25.40.180	Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat ›	0.53	40.0	3.42e-01	78.4%	64.2%
1yc9A01	1.20.1600.10	Mainly Alpha › Up-down Bundle › Outer membrane efflux proteins (OEP) › Outer membrane efflux proteins (OEP)	0.53	33.0	2.52e-01	86.3%	27.2%
7pyvC02	3.10.20.90	Alpha Beta › Roll › Ubiquitin-like (UB roll) › Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1	0.53	26.0	3.44e-01	75.5%	90.0%
1st6A01	1.20.120.810	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Vinculin, Vh2 four-helix bundle	0.52	37.0	3.09e-01	75.5%	47.5%
1g4uS01	1.20.120.260	Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Virulence factor YopE uncharacterised domain	0.51	39.0	4.05e-01	79.1%	90.6%
1lkvX02	1.10.220.30	Mainly Alpha › Orthogonal Bundle › Annexin V; domain 1 › Flagellar motor switch protein FliG, alpha-alpha superhelical domain	0.51	40.0	4.16e-01	85.6%	88.6%
1abvA00	1.10.520.20	Mainly Alpha › Orthogonal Bundle › Peroxidase; domain 1 › N-terminal domain of the delta subunit of the F1F0-ATP synthase	0.50	27.0	3.07e-01	99.3%	65.7%

ECOD (18)

UID	F-ID	Classification	TM-score	Bits	E-value	Q cov	T cov
3543503	170.2.1.1 ↗	alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain › Gag_p24	0.94	90.0	8.53e-01	100.0%	95.0%
3866760	170.2.1.1 ↗	alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain › Gag_p24	0.92	87.0	8.69e-01	97.8%	96.4%
2126757	170.2.1.1 ↗	alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain › Gag_p24	0.90	85.0	8.57e-01	99.3%	98.6%
1678502	170.2.1.1 ↗	alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain › Gag_p24	0.89	79.0	7.21e-01	93.5%	100.0%
56909	170.2.1.0 ↗	alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain	0.89	79.0	7.75e-01	92.8%	97.3%
4057	170.2.1.0 ↗	alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain	0.78	65.0	6.69e-01	86.3%	100.0%
1558678	170.2.1.1 ↗	alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain › Gag_p24	0.78	64.0	6.85e-01	99.3%	100.0%
140763	170.2.1.0 ↗	alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain	0.78	70.0	7.13e-01	99.3%	100.0%
2138586	170.2.1.0 ↗	alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain	0.77	71.0	7.10e-01	99.3%	97.1%
145205	170.2.1.1 ↗	alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain › Gag_p24	0.77	70.0	6.90e-01	99.3%	98.7%
140713	170.2.1.0 ↗	alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain	0.75	70.0	6.94e-01	99.3%	96.5%
3373091	221.1.1.2 ↗	a+b two layers › beta-Grasp › Ubiquitin-related › Ubiquitin-like › ubiquitin	0.59	18.0	2.93e-01	96.4%	72.0%
3865596	3745.1.1.1 ↗	alpha bundles › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Sodium/Calcium exchanger › Na_Ca_ex	0.58	45.0	3.16e-01	81.3%	100.0%
3643035	193.1.1.0 ↗	alpha bundles › CH domain-like › Calponin-homology domain-like › Calponin-homology domain-like	0.54	39.0	3.15e-01	73.4%	43.8%
4325826	225.1.1.27 ↗	a+b two layers › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase-like › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase › PF26329	0.53	44.0	3.57e-01	87.8%	86.1%
3688312	5050.1.1.9 ↗	alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › MFS_1	0.51	46.0	3.67e-01	100.0%	58.0%
3705859	109.4.1.1315 ↗	alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_7, TPR_8, TPR_10, TPR_12	0.50	36.0	3.07e-01	74.8%	78.7%
3412831	7015.1.1.0 ↗	alpha bundles › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain › Palmitoyltransferase DHHC transmembrane domain	0.50	31.0	3.08e-01	89.9%	56.7%

D3 medium residues 447-562

PDB

Domain cluster: rep: p24_CA__NP_955618__Human_T-cell_leukemia_virus_type_I__11908__D133-202

Pfam (1)

Accession	Name	Score	E-value	Q cov	HMM cov
PF19317.5 best	Gag_p24_C	78.2	4.30e-22	58.6%	89.2%