6R8C: HIV capsid hexamer with IP5 ligand

HIV capsid hexamer with IP5 ligand. Determined by X-ray diffraction at 1.92 Å resolution. Released 6 May 2020.

Method: X-ray diffraction
Resolution: 1.92 Å
Organism: Human immunodeficiency virus 1
Chains: 1
Atoms: 1,840
Mol. weight: 23.55 kDa
Ligands: 5MY
Released: 6 May 2020

Explore 6R8C in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6R8C contains 14 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: 14 helices, 2 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
α-helix	95-99	5
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	189-192	4
α-helix	196-204	9
α-helix	211-217	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gag polyprotein	A	protein	205	Human immunodeficiency virus 1	B6DRA0

Sequence of entity 1 (A), FASTA

>6R8C_1 Gag polyprotein (chains A)
PIVQNLQGQMVHQCISPRTLNAWVKVVEEKAFSPEVIPMFSALSCGATPQDLNTMLNTVG
GHQAAMQMLKETINEEAAEWDRLHPVHIAPGQMREPRGSDIAGTTSTLQEQIGWMTHNPP
IPVGEIYKRWIILGLNKIVRMYSPTSILDIRQGPKEPFRDYVDRFYKTLRAEQTLLVQNA
NPDCKTILKALGPGATLEEMMTACQ

Ligands and cofactors

ID	Name	Formula	Copies
5MY	Myo-inositol-(1,3,4,5,6)-pentakisphosphate	C6 H17 O21 P5	1

Primary citation

HIV hexamer. James, L.C. To be published.

Other PDB entries of the same protein (UniProt B6DRA0), best resolution first:

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

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