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gag_polyprotein

Euk-Vir

Bovine_immunodeficiency_virus

gag_polyprotein__NP_040562__Bovine_immunodeficiency_virus__11657

Identity

Accession:
NP_040562 ↗
Protein ID:
gag_polyprotein
Kingdom:
euk

Quality

57.8 mean pLDDT

Taxonomy

Pararnavirae› Artverviricota› Revtraviricetes› Ortervirales› Retroviridae› Lentivirus› Bovine_immunodeficiency_virus

TaxID: 11657

Cluster

View cluster (3 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 159-282
PDB
Domain cluster: rep: gag_protein__YP_009305199__Simian_retrovirus_8__1904439__D302-440
CATH (32)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
1eiaA01 1.10.375.10 Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein 0.88 84.0 8.15e-01 98.4% 97.7%
2xgvA00 1.10.375.10 Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein 0.87 81.0 7.92e-01 99.2% 91.7%
2xguB00 1.10.375.10 Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein 0.86 81.0 7.89e-01 98.4% 91.8%
1l6nA02 1.10.375.10 Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein 0.85 76.0 7.50e-01 95.2% 99.2%
1u7kA00 1.10.375.10 Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein 0.71 65.0 6.36e-01 97.6% 91.6%
2lhrA00 1.20.58.1270 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.70 35.0 4.26e-01 100.0% 74.4%
8b9zK01 1.10.287.3510 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › 0.63 38.0 4.31e-01 100.0% 81.3%
3s0xA01 1.20.120.1220 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.57 43.0 4.11e-01 79.8% 72.8%
6xz3A01 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.57 45.0 4.69e-01 85.5% 100.0%
1h6gA02 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.56 45.0 4.59e-01 86.3% 99.2%
2ovjA00 1.10.555.10 Mainly Alpha › Orthogonal Bundle › Phosphatidylinositol 3-kinase; Chain A › Rho GTPase activation protein 0.56 36.0 3.08e-01 84.7% 39.3%
8gy0A01 1.10.600.10 Mainly Alpha › Orthogonal Bundle › Farnesyl Diphosphate Synthase › Farnesyl Diphosphate Synthase 0.56 40.0 3.12e-01 75.0% 86.5%
1nxeA02 1.10.580.10 Mainly Alpha › Orthogonal Bundle › Citrate Synthase; domain 1 › Citrate Synthase, domain 1 0.56 43.0 3.46e-01 82.3% 95.7%
3qnfA04 1.10.3480.20 Mainly Alpha › Orthogonal Bundle › TorD-like › 0.55 39.0 3.49e-01 72.6% 96.0%
1yjgA00 1.20.120.240 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Lipoprotein, type 6 0.55 45.0 4.16e-01 87.1% 85.4%
1sziA02 1.20.120.340 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Flagellar protein FliS 0.55 44.0 4.30e-01 86.3% 91.2%
1sz9C00 1.25.40.90 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.55 38.0 3.71e-01 71.8% 89.3%
3caxA01 1.20.120.520 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › nmb1532 protein domain like 0.54 44.0 3.66e-01 87.1% 59.9%
2hkuB00 1.10.357.10 Mainly Alpha › Orthogonal Bundle › Tetracycline Repressor; domain 2 › Tetracycline Repressor, domain 2 0.54 41.0 3.62e-01 79.0% 83.8%
4jxtA00 1.25.40.90 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › 0.53 37.0 3.68e-01 72.6% 67.7%
8cdaC01 1.10.540.10 Mainly Alpha › Orthogonal Bundle › Butyryl-Coa Dehydrogenase, subunit A; domain 1 › Acyl-CoA dehydrogenase/oxidase, N-terminal domain 0.53 45.0 4.68e-01 93.5% 98.3%
3o6xA02 1.20.120.1560 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › 0.52 37.0 3.50e-01 72.6% 77.7%
3ddlA00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.52 43.0 3.41e-01 87.9% 84.1%
1dowA00 1.20.120.230 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Alpha-catenin/vinculin-like 0.52 42.0 3.54e-01 85.5% 55.1%
2hivA01 1.10.3260.10 Mainly Alpha › Orthogonal Bundle › DNA ligase i, domain 1 › DNA ligase, ATP-dependent, N-terminal domain 0.52 42.0 3.46e-01 84.7% 95.9%
4o6mA02 1.20.120.1760 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CDP-alcohol phosphotransferase transmembrane (TM) domain 0.52 46.0 3.99e-01 98.4% 74.4%
6k6iA00 1.20.1070.10 Mainly Alpha › Up-down Bundle › Rhopdopsin 7-helix transmembrane proteins › Rhodopsin 7-helix transmembrane proteins 0.52 42.0 3.52e-01 87.9% 89.5%
4xpwA00 1.20.120.50 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Hemerythrin-like 0.52 41.0 4.07e-01 85.5% 85.5%
4mndA02 1.20.120.1760 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › CDP-alcohol phosphotransferase transmembrane (TM) domain 0.52 46.0 3.98e-01 98.4% 68.6%
3cqcA00 1.20.190.50 Mainly Alpha › Up-down Bundle › Delta-Endotoxin; domain 1 › 0.51 39.0 3.09e-01 79.8% 86.6%
1hw1A02 1.20.120.530 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › GntR ligand-binding domain-like 0.51 42.0 3.99e-01 91.9% 98.7%
4gyoA02 1.25.40.10 Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain 0.50 37.0 3.09e-01 76.6% 68.6%
ECOD (19)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
4057 170.2.1.0 ↗ alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain 0.90 83.0 8.15e-01 96.0% 98.5%
2138586 170.2.1.0 ↗ alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain 0.88 84.0 8.03e-01 100.0% 90.7%
140713 170.2.1.0 ↗ alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain 0.88 83.0 7.80e-01 98.4% 88.8%
140763 170.2.1.0 ↗ alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain 0.87 81.0 7.92e-01 99.2% 91.7%
56881 170.2.1.0 ↗ alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain 0.84 79.0 7.41e-01 99.2% 91.7%
145205 170.2.1.1 ↗ alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain › Gag_p24 0.81 75.0 7.06e-01 99.2% 89.9%
3616859 532.2.1.0 ↗ alpha arrays › Type III secretion system domain-like › Type III secretion system domains › Type III secretion system domains 0.67 40.0 5.01e-01 70.2% 97.3%
3414696 109.4.1.192 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_8 0.60 35.0 2.97e-01 73.4% 32.9%
3352030 109.4.1.0 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat 0.60 42.0 2.95e-01 72.6% 31.6%
3778922 109.4.1.517 ↗ alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › Med24_N 0.58 40.0 3.24e-01 71.8% 58.0%
3474227 601.1.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › Vinculin 0.57 46.0 4.54e-01 86.3% 91.1%
3909060 4229.1.1.1 ↗ alpha bundles › Indolic compounds 2,3-dioxygenase-like › Indolic compounds 2,3-dioxygenase-like › Indolic compounds 2,3-dioxygenase-like › IDO 0.56 39.0 3.04e-01 72.6% 84.9%
5041317 601.30.1.1 ↗ alpha bundles › Four-helical up-and-down bundle › Helical bundle domain in hypothetical protein PH1320 › Helical bundle domain in hypothetical protein PH1320 › NOG1_N 0.56 45.0 4.54e-01 86.3% 93.6%
4478396 192.29.1.24 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) › TMEM237 0.56 45.0 3.99e-01 87.1% 80.0%
3377613 108.1.1.0 ↗ alpha arrays › EF-hand › EF-hand-related › EF-hand 0.55 45.0 4.72e-01 86.3% 99.1%
5020411 601.4.1.0 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains 0.53 43.0 4.03e-01 85.5% 78.7%
4019686 4121.1.1.1 ↗ a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like › CorA 0.53 46.0 3.40e-01 100.0% 37.1%
4972725 3883.1.1.1 ↗ alpha bundles › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-alcohol phosphotransferase helical bundle domain › CDP-OH_P_transf 0.52 46.0 4.02e-01 99.2% 73.3%
3197084 601.4.1.34 ↗ alpha bundles › Four-helical up-and-down bundle › Histidine kinase associated sensor domains › Histidine kinase associated sensor domains › SHR3_chaperone 0.51 41.0 3.66e-01 87.1% 83.2%
D2 high residues 287-374
PDB
Domain cluster: rep: gag_precursor__NP_042684__Jembrana_disease_virus__36370__D282-354
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF19317.5 best Gag_p24_C 67.2 1.20e-18 76.1% 86.5%
D3 medium residues 3-116
PDB