9S6O: HIV-1 capsid (M-group) - native

HIV-1 capsid (M-group) - native in complex with JW3-076. Determined by X-ray diffraction at 2.09 Å resolution. Released 12 Aug 2026.

Method: X-ray diffraction
Resolution: 2.09 Å
Organism: Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)
Chains: 1
Atoms: 1,822
Mol. weight: 26.6 kDa
Ligands: A1JL3
Released: 12 Aug 2026

Explore 9S6O in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9S6O contains 16 α-helices and 2 β-strands across 1 chain. 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: 16 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	1
β-strand	11-12	2	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
α-helix	85-88	4
α-helix	90-92	3
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	161-173	13
α-helix	179-192	14
α-helix	196-204	9
α-helix	211-217	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gag polyprotein	A	protein	231	Human immunodeficiency virus type 1 (NEW YORK-5 ISOLATE)	B6DRA0

Sequence of entity 1 (A), FASTA

>9S6O_1 Gag polyprotein (chains A)
PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVG
GHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTH
NPPIPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQASQE
VKNWMTETLLVQNANPDCKTILKALGPGATLEEMMTACQGVGGPGHKARVL

Ligands and cofactors

ID	Name	Formula	Copies
A1JL3	(2~{S})-3-[3,5-difluorophenyl)ethyl]-~{N}-(4-methoxyphenyl)-~{N}-methyl-2-[2-(2…	C28 H27 F2 N3 O3	1

Water and common crystallization additives (IOD, CL, BME) are not listed.

Primary citation

Cofactor-mimicking HIV-1 capsid inhibitors, and their escape mutants, drive innate immune sensing. Govasli, M.A.L., Pinotsis, N., Towers, G. et al. To be published.

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
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
9PGS 2.4 Å, HIV Capsid Hexamer bound to Compound 6
9S6J 2.4 Å, HIV-1 capsid (M-group) - CPSF6

Browse structure collections

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