9PGS: HIV Capsid Hexamer
HIV Capsid Hexamer bound to Compound 6. Determined by X-ray diffraction at 2.4 Å resolution. Released 8 Oct 2025.
- Method
- X-ray diffraction
- Resolution
- 2.4 Å
- Organism
- Human immunodeficiency virus 1
- Chains
- 12
- Atoms
- 20,550
- Mol. weight
- 313.03 kDa
- Ligands
- A1CH4
- Released
- 8 Oct 2025
Explore 9PGS in 3D
Show helices and sheets
RCSB PDB
PDBe
Secondary structure: helices and β-sheets
9PGS contains 183 α-helices and 34 β-strands across 12 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.
Chain A: 13 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 1 |
| β-strand | 10-12 | 3 | 1 |
| α-helix | 14-16 | 3 | |
| α-helix | 17-30 | 14 | |
| α-helix | 36-43 | 8 | |
| α-helix | 49-57 | 9 | |
| α-helix | 63-83 | 21 | |
| β-strand | 91 | 1 | 2 |
| α-helix | 97-99 | 3 | |
| α-helix | 101-104 | 4 | |
| α-helix | 111-118 | 8 | |
| α-helix | 126-145 | 20 | |
| α-helix | 161-175 | 15 | |
| α-helix | 184-192 | 9 | |
| α-helix | 196-204 | 9 | |
| α-helix | 211-217 | 7 | |
Chain B: 15 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 3 |
| β-strand | 10-12 | 3 | 3 |
| α-helix | 14-16 | 3 | |
| α-helix | 17-30 | 14 | |
| α-helix | 36-43 | 8 | |
| α-helix | 49-57 | 9 | |
| α-helix | 63-83 | 21 | |
| α-helix | 95 | 1 | |
| β-strand | 96 | 1 | 4 |
| α-helix | 97-99 | 3 | |
| α-helix | 101-105 | 5 | |
| α-helix | 111-118 | 8 | |
| α-helix | 126-145 | 20 | |
| α-helix | 150-152 | 3 | |
| α-helix | 161-176 | 16 | |
| α-helix | 184-192 | 9 | |
| α-helix | 196-204 | 9 | |
| α-helix | 211-217 | 7 | |
Chain C: 15 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 5 |
| β-strand | 10-12 | 3 | 5 |
| α-helix | 14-16 | 3 | |
| α-helix | 17-30 | 14 | |
| α-helix | 36-43 | 8 | |
| α-helix | 49-57 | 9 | |
| α-helix | 63-83 | 21 | |
| α-helix | 95 | 1 | |
| β-strand | 96 | 1 | 6 |
| α-helix | 97-99 | 3 | |
| α-helix | 101-104 | 4 | |
| α-helix | 111-119 | 9 | |
| α-helix | 126-145 | 20 | |
| α-helix | 150-152 | 3 | |
| α-helix | 161-175 | 15 | |
| α-helix | 184-192 | 9 | |
| α-helix | 196-205 | 10 | |
| α-helix | 211-217 | 7 | |
Chain D: 14 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 7 |
| β-strand | 10-12 | 3 | 7 |
| α-helix | 14-16 | 3 | |
| α-helix | 17-30 | 14 | |
| α-helix | 36-43 | 8 | |
| α-helix | 49-57 | 9 | |
| α-helix | 63-83 | 21 | |
| α-helix | 97-99 | 3 | |
| α-helix | 101-105 | 5 | |
| α-helix | 111-118 | 8 | |
| α-helix | 126-144 | 19 | |
| α-helix | 150-152 | 3 | |
| α-helix | 161-175 | 15 | |
| α-helix | 184-192 | 9 | |
| α-helix | 196-205 | 10 | |
| α-helix | 211-217 | 7 | |
Chain E: 16 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 8 |
| β-strand | 10-12 | 3 | 8 |
| α-helix | 14-16 | 3 | |
| α-helix | 17-30 | 14 | |
| α-helix | 36-43 | 8 | |
| α-helix | 49-57 | 9 | |
| α-helix | 63-83 | 21 | |
| α-helix | 85-88 | 4 | |
| α-helix | 90 | 1 | |
| β-strand | 91 | 1 | 9 |
| α-helix | 92 | 1 | |
| α-helix | 97-99 | 3 | |
| α-helix | 101-104 | 4 | |
| α-helix | 111-119 | 9 | |
| α-helix | 126-145 | 20 | |
| α-helix | 161-176 | 16 | |
| α-helix | 184-192 | 9 | |
| α-helix | 196-205 | 10 | |
| α-helix | 211-217 | 7 | |
Chain F: 17 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 10 |
| β-strand | 10-12 | 3 | 10 |
| α-helix | 14-16 | 3 | |
| α-helix | 17-30 | 14 | |
| α-helix | 36-43 | 8 | |
| α-helix | 49-57 | 9 | |
| α-helix | 63-83 | 21 | |
| α-helix | 85-88 | 4 | |
| α-helix | 90 | 1 | |
| β-strand | 91 | 1 | 11 |
| α-helix | 92 | 1 | |
| α-helix | 97-99 | 3 | |
| α-helix | 101-104 | 4 | |
| α-helix | 111-118 | 8 | |
| α-helix | 126-145 | 20 | |
| α-helix | 150-152 | 3 | |
| α-helix | 161-175 | 15 | |
| α-helix | 184-192 | 9 | |
| α-helix | 196-203 | 8 | |
| α-helix | 211-217 | 7 | |
Chain G: 15 helices, 3 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 12 |
| β-strand | 10-12 | 3 | 12 |
| α-helix | 14-16 | 3 | |
| α-helix | 17-30 | 14 | |
| α-helix | 36-43 | 8 | |
| α-helix | 49-57 | 9 | |
| α-helix | 63-83 | 21 | |
| α-helix | 95 | 1 | |
| β-strand | 96 | 1 | 9 |
| α-helix | 97-99 | 3 | |
| α-helix | 101-104 | 4 | |
| α-helix | 111-118 | 8 | |
| α-helix | 126-144 | 19 | |
| α-helix | 150-152 | 3 | |
| α-helix | 161-175 | 15 | |
| α-helix | 187-192 | 6 | |
| α-helix | 196-205 | 10 | |
| α-helix | 211-217 | 7 | |
Chain H: 16 helices, 2 β-strands
| Element | Residues | Length | Sheet |
|---|
| β-strand | 2-4 | 3 | 13 |
| β-strand | 10-12 | 3 | 13 |
| α-helix | 14-16 | 3 | |
| α-helix | 17-30 | 14 | |
| α-helix | 36-43 | 8 | |
| α-helix | 51-57 | 7 | |
| α-helix | 63-83 | 21 | |
| α-helix | 85-88 | 4 | |
| α-helix | 90-92 | 3 | |
| α-helix | 97-99 | 3 | |
| α-helix | 101-104 | 4 | |
| α-helix | 111-119 | 9 | |
| α-helix | 126-145 | 20 | |
| α-helix | 150-152 | 3 | |
| α-helix | 161-175 | 15 | |
| α-helix | 184-192 | 9 | |
| α-helix | 196-205 | 10 | |
| α-helix | 211-217 | 7 | |
4 more chain groups are not listed. Open the entry in the viewer and use the sequence panel to see them.
Molecules and chains
| Molecule | Chains | Type | Length | Organism | UniProt |
|---|
| HIV-1 capsid | A, B, C, D, E, F, G, H, I, J, K, L | protein | 232 | Human immunodeficiency virus 1 | B6DRA0 |
Sequence of entity 1 (A, B, C, D, E, F, G, H, I, J, K, L), FASTA
>9PGS_1 HIV-1 capsid (chains A, B, C, D, E, F, G, H, I, J, K, L)
MPIVQNLQGQMVHQCISPRTLNAWVKVVEEKAFSPEVIPMFSALSCGATPQDLNTMLNTV
GGHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMT
HNPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQ
EVKNAATETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL
Ligands and cofactors
| ID | Name | Formula | Copies |
|---|
| A1CH4 | 3,5-difluoro-Nalpha-[(5-hydroxy-1H-indol-3-yl)acetyl]-N-(4-methoxyphenyl)-N-met… | C27 H25 F2 N3 O4 | 12 |
Primary citation
Discovery of Lenacapavir: First-in-Class Twice-Yearly Capsid Inhibitor for HIV-1 Treatment and Pre-exposure Prophylaxis. Canales, E., Tse, W., Schroeder, S.D. et al. J Med Chem (2025) 68:21072-21094. DOI 10.1021/acs.jmedchem.5c01625 · PubMed
Other PDB entries of the same protein (UniProt B6DRA0), best resolution first:
- 6R8C 1.92 Å, HIV capsid hexamer with IP5 ligand
- 9RPC 1.97 Å, HIV-1 capsid (M-group) - native
- 7RMM 1.97 Å, Structure of N74D mutant of disulfide stabilized HIV-1 CA hexamer
- 6ERM 2.0 Å, HIV Hexamer with ligand
- 9S6W 2.07 Å, HIV-1 capsid (M-group) - native in complex with JW3-100
- 9S6O 2.09 Å, HIV-1 capsid (M-group) - native in complex with JW3-076
- 9PGT 2.2 Å, HIV Capsid Hexamer bound to Compound 12
- 7RMJ 2.27 Å, Disulfide stabilized HIV-1 CA hexamer in complex with capsid inhibitor…
- 9PGV 2.3 Å, HIV Capsid Hexamer bound to Compound 24
- 6ERN 2.36 Å, HIV Hexamer with ligand
- 9S6V 2.36 Å, HIV-1 capsid (M-group) - native in complex with JW3-094
- 9S6J 2.4 Å, HIV-1 capsid (M-group) - CPSF6
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