←Back to structures
uncovered_polypeptide_Gag-Pol
Euk-VirHuman_immunodeficiency_virus_1
uncovered_polypeptide_Gag-Pol__NP_057849_0-431__Human_immunodeficiency_virus_1__11676
Identity
- Accession:
- NP_057849_0-431 ↗
- Protein ID:
- uncovered_polypeptide_Gag-Pol
- Kingdom:
- euk
Quality
71.9
mean pLDDT
Taxonomy
Pararnavirae›
Artverviricota›
Revtraviricetes›
Ortervirales›
Retroviridae›
Lentivirus›
Human_immunodeficiency_virus_1
TaxID: 11676
Cluster
View cluster (4 members)3D Structure
Domains
high = three domain segmentations agree, medium = two domain segmentations agree. Numbered high-first then medium, N→C within each tier.
D1
high
residues 11-113
D2
high
residues 144-217_229-277
Domain cluster:
rep: gag_protein__YP_009305199__Simian_retrovirus_8__1904439__D302-440
Pfam (1)
| Accession | Name | Score | E-value | Q cov | HMM cov |
|---|---|---|---|---|---|
| PF00607.26 best | Gag_p24 | 48.3 | 1.40e-12 | 95.9% | 85.2% |
CATH (14)
| Domain ID | Class ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 1l6nA02 | 1.10.375.10 | Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein | 0.93 | 86.0 | 8.40e-01 | 95.9% | 98.5% |
| 2xgvA00 | 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 | 8.13e-01 | 100.0% | 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 | 0.85 | 81.0 | 7.88e-01 | 100.0% | 92.5% |
| 1eiaA01 | 1.10.375.10 | Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein | 0.85 | 79.0 | 7.72e-01 | 98.4% | 97.0% |
| 1d1dA01 | 1.10.375.10 | Mainly Alpha › Orthogonal Bundle › Human Immunodeficiency Virus Type 1 Capsid Protein › Human Immunodeficiency Virus Type 1 Capsid Protein | 0.73 | 67.0 | 6.44e-01 | 100.0% | 97.9% |
| 2af7D00 | 1.20.1290.10 | Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like | 0.57 | 33.0 | 3.38e-01 | 92.7% | 55.4% |
| 2lniA00 | 1.25.40.10 | Mainly Alpha › Alpha Horseshoe › Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat › Tetratricopeptide repeat domain | 0.57 | 33.0 | 3.29e-01 | 71.5% | 51.1% |
| 5dikA00 | 1.20.1290.10 | Mainly Alpha › Up-down Bundle › AhpD-like › AhpD-like | 0.57 | 33.0 | 3.49e-01 | 91.1% | 61.6% |
| 1fntc01 | 1.20.120.180 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › Proteasome activator pa28, C-terminal domain | 0.56 | 45.0 | 3.97e-01 | 87.8% | 86.2% |
| 2e87A01 | 1.20.120.1190 | Mainly Alpha › Up-down Bundle › Four Helix Bundle (Hemerythrin (Met), subunit A) › | 0.55 | 45.0 | 4.14e-01 | 87.8% | 90.0% |
| 4l3tA04 | 3.30.830.10 | Alpha Beta › 2-Layer Sandwich › Cytochrome Bc1 Complex; Chain A, domain 1 › Metalloenzyme, LuxS/M16 peptidase-like | 0.53 | 38.0 | 2.97e-01 | 74.0% | 54.0% |
| 5domA00 | 1.10.110.10 | Mainly Alpha › Orthogonal Bundle › Hydrophobic Seed Protein › Plant lipid-transfer and hydrophobic proteins | 0.50 | 34.0 | 3.90e-01 | 91.1% | 95.6% |
| 2jo7A00 | 1.10.4170.10 | Mainly Alpha › Orthogonal Bundle › Glycosylphosphatidylinositol-anchored merozoite surface protein › Glycosylphosphatidylinositol-anchored merozoite surface protein | 0.50 | 41.0 | 3.43e-01 | 89.4% | 91.5% |
| 4mduA02 | 1.10.220.10 | Mainly Alpha › Orthogonal Bundle › Annexin V; domain 1 › Annexin | 0.50 | 32.0 | 3.77e-01 | 89.4% | 96.3% |
ECOD (19)
| UID | F-ID | Classification | TM-score | Bits | E-value | Q cov | T cov |
|---|---|---|---|---|---|---|---|
| 56881 | 170.2.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain | 0.99 | 98.0 | 9.07e-01 | 100.0% | 92.4% |
| 145205 | 170.2.1.1 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain › Gag_p24 | 0.91 | 86.0 | 7.99e-01 | 100.0% | 89.9% |
| 140763 | 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 | 8.13e-01 | 100.0% | 91.7% |
| 140713 | 170.2.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain | 0.87 | 83.0 | 7.86e-01 | 100.0% | 90.2% |
| 2138586 | 170.2.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain | 0.87 | 83.0 | 7.89e-01 | 100.0% | 90.0% |
| 4057 | 170.2.1.0 ↗ | alpha bundles › Retrovirus capsid protein › Retrovirus capsid protein N-terminal domain › Retrovirus capsid protein N-terminal domain | 0.86 | 80.0 | 7.84e-01 | 97.6% | 100.0% |
| 3702110 | 593.1.1.0 ↗ | alpha bundles › GroEL equatorial domain-like › GroEL equatorial domain-like › GroEL equatorial domain-like | 0.56 | 45.0 | 3.57e-01 | 87.0% | 56.2% |
| 4581508 | 601.19.1.1 ↗ | alpha bundles › Four-helical up-and-down bundle › Apolipoprotein › Apolipoprotein › Apolipoprotein | 0.55 | 43.0 | 3.63e-01 | 83.7% | 85.7% |
| 3644387 | 601.1.2.81 ↗ | alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › I/LWEQ domain (Pfam 01608) › Serinc | 0.55 | 35.0 | 3.26e-01 | 72.4% | 52.0% |
| 3891314 | 593.1.1.1 ↗ | alpha bundles › GroEL equatorial domain-like › GroEL equatorial domain-like › GroEL equatorial domain-like › Cpn60_TCP1 | 0.55 | 44.0 | 3.56e-01 | 87.0% | 53.3% |
| 3731650 | 176.1.1.0 ↗ | alpha arrays › Annexin › Annexin › Annexin | 0.54 | 36.0 | 4.12e-01 | 70.7% | 97.6% |
| 3610395 | 138.1.1.0 ↗ | alpha arrays › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain › DNA polymerase III clamp loader subunits, C-terminal domain | 0.54 | 46.0 | 4.76e-01 | 100.0% | 100.0% |
| 5027915 | 5058.1.1.0 ↗ | alpha bundles › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region › Mechanosensitive channel protein MscS (YggB), transmembrane region | 0.54 | 31.0 | 3.90e-01 | 83.7% | 94.7% |
| 3504179 | 109.4.1.198 ↗ | alpha superhelices › Repetitive alpha hairpins › ARM repeat › ARM repeat › TPR_12 | 0.53 | 34.0 | 3.44e-01 | 71.5% | 64.2% |
| 3923629 | 611.3.1.0 ↗ | alpha bundles › N-cbl like › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 › Conserved domain common to transcription factors TFIIS, elongin A, CRSP70 | 0.52 | 38.0 | 4.03e-01 | 76.4% | 100.0% |
| 5047855 | 192.29.1.0 ↗ | alpha bundles › Long alpha-hairpin › bMERB domain (bivalent Mical/EHBP Rab binding) › bMERB domain (bivalent Mical/EHBP Rab binding) | 0.52 | 43.0 | 4.10e-01 | 89.4% | 89.7% |
| 3686562 | 4121.1.1.0 ↗ | a+b three layers › CorA soluble domain-like › CorA soluble domain-like › CorA soluble domain-like | 0.51 | 46.0 | 3.24e-01 | 100.0% | 44.6% |
| 5053142 | 101.1.2.0 ↗ | alpha arrays › HTH › HTH › winged helix domain | 0.51 | 30.0 | 3.11e-01 | 97.6% | 60.0% |
| 3189820 | 601.1.1.80 ↗ | alpha bundles › Four-helical up-and-down bundle › alpha-catenin-related › alpha-catenin/vinculin › SHR3_chaperone | 0.51 | 41.0 | 3.71e-01 | 87.8% | 92.9% |
D3
medium
residues 295-364
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 | 82.0 | 2.80e-23 | 78.6% | 74.3% |