HIV-1 wild type protease with GRL-04315A, a tetrahydronaphthalene carboxamide with (R)-Boc-amine and (S)-hydroxyl functionalities as the P2 ligand. Determined by X-ray diffraction at 1.14 Å resolution. Released 31 Oct 2018.
Explore 6DV4 in 3D Show helices and sheets RCSB PDB PDBe
6DV4 contains 2 α-helices and 18 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 2-3 | 2 | 1 |
| β-strand | 10-15 | 6 | 2 |
| β-strand | 18-24 | 7 | 2 |
| β-strand | 31-33 | 3 | 2 |
| β-strand | 42-49 | 8 | 2 |
| β-strand | 52-66 | 15 | 2 |
| β-strand | 69-77 | 9 | 2 |
| β-strand | 84-85 | 2 | 2 |
| α-helix | 87-90 | 4 | |
| β-strand | 96-98 | 3 | 1 |
| Element | Residues | Length | Sheet |
|---|---|---|---|
| β-strand | 2-3 | 2 | 1 |
| β-strand | 10-15 | 6 | 3 |
| β-strand | 18-24 | 7 | 3 |
| β-strand | 32-33 | 2 | 3 |
| β-strand | 43-49 | 7 | 3 |
| β-strand | 52-66 | 15 | 3 |
| β-strand | 69-77 | 9 | 3 |
| β-strand | 84-85 | 2 | 3 |
| α-helix | 87-90 | 4 | |
| β-strand | 96-98 | 3 | 1 |
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|---|---|---|---|---|
| Protease | A, B | protein | 99 | Human immunodeficiency virus 1 | P04585 (AlphaFold model) |
>6DV4_1 Protease (chains A, B) PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFIKVRQYD QIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF
| ID | Name | Formula | Copies |
|---|---|---|---|
| GA5 | tert-butyl [(1R,4S)-4-hydroxy-7-{[(2S,3R)-3-hydroxy-4-{[(4-methoxyphenyl)sulfon… | C37 H49 N3 O8 S | 1 |
Water and common crystallization additives (NA, CL, ACT, GOL) are not listed.
Design, synthesis, and X-ray studies of potent HIV-1 protease inhibitors incorporating aminothiochromane and aminotetrahydronaphthalene carboxamide derivatives as the P2 ligands. Ghosh, A.K., Jadhav, R.D., Simpson, H. et al. Eur J Med Chem (2018) 160:171-182. DOI 10.1016/j.ejmech.2018.09.046 · PubMed
Other PDB entries of the same protein (UniProt P04585 (AlphaFold model), which also has an AlphaFold model), best resolution first:
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