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vpx_protein

Euk-Vir

Simian_immunodeficiency_virus_SIV-mnd_2

vpx_protein__NP_758889__Simian_immunodeficiency_virus_SIV-mnd_2__159122

Identity

Accession:
NP_758889 ↗
Protein ID:
vpx_protein
Kingdom:
euk

Quality

82.0 mean pLDDT

Taxonomy

Pararnavirae› Artverviricota› Revtraviricetes› Ortervirales› Retroviridae› Lentivirus› Simian_immunodeficiency_virus_SIV-mnd_2

TaxID: 159122

Cluster

View cluster (6 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 20-82
PDB
Domain cluster: rep: vpr_protein__NP_056841__Human_immunodeficiency_virus_2__11709__D23-79
Pfam (1)
AccessionNameScoreE-valueQ covHMM cov
PF00522.24 best VPR 64.9 8.00e-18 100.0% 68.7%
CATH (40)
Domain IDClass IDClassificationTM-scoreBitsE-valueQ covT cov
4cc9B00 1.20.5.4730 Mainly Alpha › Up-down Bundle › Single alpha-helices involved in coiled-coils or other helix-helix interfaces › 0.96 91.0 7.65e-01 100.0% 64.3%
2w02B01 1.10.150.640 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › AcsD, thumb domain, helical bundle 0.78 57.0 5.37e-01 76.2% 87.8%
1iuqA01 1.10.1200.50 Mainly Alpha › Orthogonal Bundle › Non-ribosomal Peptide Synthetase Peptidyl Carrier Protein; Chain A › Glycerol-3-phosphate acyltransferase, alpha helical bundle, N-terminal 0.73 63.0 5.95e-01 96.8% 89.5%
2i5uA00 1.10.10.630 Mainly Alpha › Orthogonal Bundle › Arc Repressor Mutant, subunit A › DnaD domain-like 0.73 59.0 5.52e-01 90.5% 71.4%
4m70B00 1.10.246.200 Mainly Alpha › Orthogonal Bundle › Serum Albumin; Chain A, Domain 1 › WPP domain 0.72 59.0 5.27e-01 92.1% 86.8%
3ufeA02 1.20.58.1950 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.71 54.0 5.82e-01 98.4% 98.1%
3a06B03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.70 58.0 5.19e-01 95.2% 65.9%
2y1eA03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.69 58.0 5.27e-01 98.4% 69.0%
1wn0A00 1.20.120.160 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › HPT domain 0.68 49.0 3.84e-01 76.2% 73.3%
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 0.68 56.0 5.07e-01 98.4% 68.2%
2e62A01 6.10.140.420 Special › Helix non-globular › Helix Hairpins › 0.66 46.0 4.85e-01 74.6% 88.5%
3t46A00 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.66 60.0 5.68e-01 100.0% 92.0%
4zqeA03 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.65 56.0 4.90e-01 98.4% 65.6%
3u3iA02 1.20.58.1110 Mainly Alpha › Up-down Bundle › Methane Monooxygenase Hydroxylase; Chain G, domain 1 › 0.64 46.0 3.85e-01 76.2% 56.5%
2blfB01 1.10.760.10 Mainly Alpha › Orthogonal Bundle › Cytochrome Bc1 Complex; Chain D, domain 2 › Cytochrome c-like domain 0.63 43.0 4.33e-01 93.7% 71.4%
2ewfA02 1.20.1270.310 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.63 55.0 5.10e-01 100.0% 82.7%
5hb0D01 1.20.120.1880 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Nucleoporin, helical C-terminal domain 0.63 44.0 2.95e-01 74.6% 20.3%
1ie9A00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.62 45.0 3.00e-01 77.8% 33.3%
3vygE00 1.10.472.20 Mainly Alpha › Orthogonal Bundle › Cyclin A; domain 1 › Nitrile hydratase, beta subunit 0.62 49.0 3.91e-01 96.8% 39.7%
2mmbA00 4.10.640.20 Few Secondary Structures › Irregular › 30s Ribosomal Protein S18 › 0.61 44.0 3.78e-01 77.8% 46.7%
7qocA01 1.10.3210.10 Mainly Alpha › Orthogonal Bundle › Hypothetical protein af1432 › Hypothetical protein af1432 0.61 49.0 3.65e-01 95.2% 32.1%
1rp3A01 1.10.1740.10 Mainly Alpha › Orthogonal Bundle › Rna Polymerase Sigma Factor; Chain: A › RNA polymerase sigma factor, region 2, helix turn helix motif 0.61 52.0 4.77e-01 96.8% 78.8%
3ddhA02 1.10.150.240 Mainly Alpha › Orthogonal Bundle › DNA polymerase; domain 1 › Putative phosphatase; domain 2 0.61 47.0 4.48e-01 92.1% 72.8%
1u84A00 1.10.340.20 Mainly Alpha › Orthogonal Bundle › Endonuclease III; domain 1 › Apc36109-like domain 0.60 40.0 3.74e-01 77.8% 53.1%
1nt2B02 1.10.287.660 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › Helix hairpin bin 0.59 42.0 4.19e-01 74.6% 71.6%
1s9qA00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.59 51.0 3.53e-01 100.0% 63.4%
3sqnA02 1.10.1790.40 Mainly Alpha › Orthogonal Bundle › PTS-regulatory domain, PRD › 0.59 47.0 3.96e-01 93.7% 50.0%
3f5cB00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.59 49.0 3.61e-01 96.8% 49.7%
2pmrA00 1.20.1270.90 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › AF1782-like 0.58 49.0 4.68e-01 96.8% 93.4%
4i8oA03 1.10.8.1130 Mainly Alpha › Orthogonal Bundle › Helicase, Ruva Protein; domain 3 › Bacterial toxin RNase RnlA/LsoA, C-terminal Dmd-binding domain 0.57 47.0 4.63e-01 92.1% 91.0%
4wz9A04 1.25.50.20 Mainly Alpha › Alpha Horseshoe › Zincin-like fold › 0.57 38.0 2.49e-01 74.6% 13.5%
1xvpB00 1.10.565.10 Mainly Alpha › Orthogonal Bundle › Retinoid X Receptor › Retinoid X Receptor 0.56 46.0 3.20e-01 96.8% 67.5%
1wgwA00 1.20.120.140 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › SRP54, nucleotide-binding domain 0.55 45.0 4.01e-01 96.8% 83.8%
6ygiB01 1.10.4090.10 Mainly Alpha › Orthogonal Bundle › Hepatitis B viral capsid (hbcag) fold › Viral capsid, core domain supefamily, Hepatitis B virus 0.55 47.0 3.69e-01 100.0% 92.5%
3favD00 1.10.287.1060 Mainly Alpha › Orthogonal Bundle › Helix Hairpins › ESAT-6-like 0.55 39.0 3.72e-01 76.2% 61.5%
6a3kA00 1.20.120.10 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Cytochrome c/b562 0.54 46.0 3.66e-01 95.2% 92.2%
1dkxA02 1.20.1270.10 Mainly Alpha › Up-down Bundle › Substrate Binding Domain Of Dnak; Chain:A; Domain 2 › 0.53 45.0 4.19e-01 96.8% 82.5%
1hdlA00 3.30.60.30 Alpha Beta › 2-Layer Sandwich › Wheat Germ Agglutinin (Isolectin 2); domain 1 › 0.53 36.0 3.87e-01 92.1% 81.8%
3rh3A01 1.20.120.930 Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Uncharacterised protein PF12889, N-terminal DUF3829 0.53 48.0 3.68e-01 98.4% 49.6%
3ce2A01 1.20.140.70 Mainly Alpha › Up-down Bundle › Butyryl-CoA Dehydrogenase, subunit A; domain 3 › Oligopeptidase f, N-terminal domain 0.51 35.0 2.72e-01 71.4% 41.6%
ECOD (39)
UIDF-IDClassificationTM-scoreBitsE-valueQ covT cov
1124196 3788.1.1.1 ↗ alpha bundles › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) › Viral accessory protein x (Vpx) / viral protein r (Vpr) › VPR 0.96 91.0 7.65e-01 100.0% 64.3%
3738042 142.1.1.0 ↗ alpha complex topology › Sigma2 domain-like › Sigma2 domain of RNA polymerase sigma factors › Sigma2 domain of RNA polymerase sigma factors 0.76 54.0 5.28e-01 79.4% 67.1%
3997160 632.7.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain 0.72 62.0 5.40e-01 100.0% 76.0%
4930612 4009.1.1.4 ↗ alpha bundles › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › alpha-helical domain in AF1104-like proteins › DUF3243 0.70 47.0 4.39e-01 76.2% 55.0%
5061320 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.70 63.0 5.80e-01 100.0% 80.0%
5060848 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.68 58.0 5.94e-01 92.1% 98.3%
5058632 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.68 60.0 5.80e-01 96.8% 88.6%
5068968 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.68 60.0 5.84e-01 98.4% 90.0%
5060022 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.66 59.0 5.55e-01 100.0% 85.3%
4981750 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.66 59.0 5.47e-01 100.0% 80.0%
4971392 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 0.66 57.0 4.09e-01 100.0% 42.5%
4027189 589.1.1.0 ↗ alpha arrays › Triger factor/SurA peptide-binding domain-like › Triger factor/SurA peptide-binding domain-like › Porin chaperone SurA, peptide-binding domain 0.66 53.0 4.69e-01 90.5% 61.1%
5068969 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.66 58.0 5.66e-01 100.0% 91.4%
5066226 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.66 55.0 5.46e-01 100.0% 90.8%
5016654 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.65 58.0 5.81e-01 100.0% 96.9%
5060146 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.65 58.0 5.76e-01 100.0% 98.5%
4942992 103.5.1.0 ↗ alpha arrays › RuvA-C › post-HMGL domain-like › post-HMGL domain-like 0.65 43.0 4.59e-01 85.7% 86.0%
5016657 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.64 57.0 5.52e-01 100.0% 90.0%
5061375 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.64 57.0 5.54e-01 100.0% 91.4%
5060141 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.63 55.0 5.36e-01 100.0% 91.3%
4492498 632.7.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › HSP70 0.63 57.0 5.23e-01 100.0% 83.7%
4951139 192.29.1.0 ↗ alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) 0.63 55.0 4.78e-01 100.0% 67.0%
3709879 181.1.1.0 ↗ alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins 0.63 52.0 4.99e-01 93.7% 85.3%
5059485 7076.1.1.0 ↗ 0.62 49.0 5.16e-01 85.7% 100.0%
4594328 181.1.1.2 ↗ alpha bundles › Domain of the SRP/SRP receptor G proteins-like › Domain of the SRP/SRP receptor G-proteins › Domain of the SRP/SRP receptor G-proteins › FlhF_N 0.62 46.0 4.39e-01 90.5% 68.0%
5061329 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.62 54.0 5.04e-01 100.0% 80.0%
4981741 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.62 51.0 5.20e-01 100.0% 100.0%
4444896 632.7.1.1 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain › HSP70 0.61 53.0 4.52e-01 100.0% 66.7%
5060021 632.11.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › AF1782-like › AF1782-like 0.60 53.0 5.33e-01 100.0% 98.5%
3437734 192.4.1.0 ↗ alpha bundles › Long alpha-hairpin › Ribosomal protein L29 (L29p) › Ribosomal protein L29 (L29p) 0.60 41.0 4.08e-01 71.4% 67.7%
1721530 632.23.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Helical linker domain in nicking endonuclease N.BspD6I › Helical linker domain in nicking endonuclease N.BspD6I 0.59 50.0 4.76e-01 100.0% 88.5%
4600933 5050.1.1.0 ↗ alpha complex topology › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter › Major facilitator superfamily (MFS) general substrate transporter 0.59 51.0 3.72e-01 100.0% 42.2%
3677185 4992.1.1.27 ↗ extended segments › RelB-like › RelB-like › RelB-like › Ist1 0.59 42.0 3.70e-01 74.6% 53.3%
5041920 632.22.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Cell division protein EzrA repeats › Cell division protein EzrA repeats 0.59 47.0 4.29e-01 93.7% 78.9%
5031855 632.15.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Staphylococcal complement inhibitor (SCIN) › Staphylococcal complement inhibitor (SCIN) 0.58 50.0 4.67e-01 100.0% 87.5%
4177393 3755.3.1.0 ↗ alpha bundles › YscO-like › CT398 helical hairpin › CT398 helical hairpin 0.58 42.0 3.17e-01 76.2% 55.9%
4036763 632.7.1.0 ↗ alpha bundles › immunoglobulin/albumin-binding domain-like › Heat shock protein 70kD (HSP70), C-terminal subdomain › Heat shock protein 70kD (HSP70), C-terminal subdomain 0.57 47.0 4.13e-01 100.0% 68.6%
4958206 3352.1.1.0 ↗ alpha bundles › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain › STT3/PglB/AglB transmembrane domain 0.56 50.0 3.10e-01 100.0% 17.6%
3590073 605.1.1.0 ↗ alpha duplicates or obligate multimers › ROP-like › Homodimeric domain of signal transducing histidine kinase › Homodimeric domain of signal transducing histidine kinase 0.53 48.0 4.36e-01 100.0% 91.8%