2XDE: Gag polyprotein

Crystal structure of the complex of PF-3450074 with an engineered HIV capsid N terminal domain. Determined by X-ray diffraction at 1.4 Å resolution. Released 22 Dec 2010.

Method: X-ray diffraction
Resolution: 1.4 Å
Organism: HUMAN IMMUNODEFICIENCY VIRUS 1
Chains: 2
Atoms: 2,569
Mol. weight: 33.29 kDa
Ligands: 1B0
Released: 22 Dec 2010

Explore 2XDE in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2XDE contains 16 α-helices and 4 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.

Chain A: 8 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	101-104	4
α-helix	111-119	9
α-helix	126-145	20

Chain B: 8 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	2-4	3	2
β-strand	10-12	3	2
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	101-104	4
α-helix	111-119	9
α-helix	126-144	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gag polyprotein	A, B	protein	145	HUMAN IMMUNODEFICIENCY VIRUS 1	P12497

Sequence of entity 1 (A, B), FASTA

>2XDE_1 GAG POLYPROTEIN (chains A, B)
MPIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTV
GGHQAAMQMLKETINEEAAEWDRLHPVGEPRGSDIAGTTSTLQEQIGWMTHNPPIPVGEI
YKRWIILGLNKIVRMYSGGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
1B0	N-methyl-nalpha-[(2-methyl-1H-indol-3-yl)acetyl]-N-phenyl-L-phenylalaninamide	C27 H27 N3 O2	2

Primary citation

HIV Capsid is a Tractable Target for Small Molecule Therapeutic Intervention. Blair, W.S., Pickford, C., Irving, S.L. et al. PLoS Pathog (2010) 6:E1220. DOI 10.1371/JOURNAL.PPAT.1001220 · PubMed

Other PDB entries of the same protein (UniProt P12497), best resolution first:

3DS4 1.12 Å, HIV-1 capsid C-terminal domain mutant (L211S) in complex with an inhibitor of particle…
3DS2 1.2 Å, HIV-1 capsid C-terminal domain mutant (Y169A)
6T6E 1.3 Å, Crystal Structure of the C-terminal domain of the HIV-1 Integrase (PNL4-3)
3L3U 1.4 Å, Crystal structure of the HIV-1 integrase core domain to 1.4A
2PWO 1.45 Å, Crystal Structure of HIV-1 CA146 A92E Psuedo Cell
3WNF 1.45 Å, Cyclic hexapeptide CKIDNC in complex with HIV-1 integrase
6OYD 1.46 Å, X-ray crystal structure of wild type HIV-1 protease in complex with GRL-004
6MCR 1.48 Å, X-ray crystal structure of wild type HIV-1 protease in complex with GRL-001
2PXR 1.5 Å, Crystal Structure of HIV-1 CA146 in the Presence of CAP-1
3WNH 1.5 Å, Cyclic hexapeptide PKZDNv in complex with HIV-1 integrase
4NX4 1.5 Å, Re-refinement of CAP-1 HIV-CA complex
6MCS 1.52 Å, X-ray crystal structure of wild type HIV-1 protease in complex with GRL-003

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