4NX4: Re-refinement of CAP-1 HIV-CA complex

Re-refinement of CAP-1 HIV-CA complex. Determined by X-ray diffraction at 1.5 Å resolution. Released 26 Feb 2014.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Human immunodeficiency virus type 1
Chains: 1
Atoms: 1,442
Mol. weight: 16.75 kDa
Ligands: ZN, JPR
Released: 26 Feb 2014

Explore 4NX4 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4NX4 contains 10 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 C: 10 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	36-42	7
α-helix	49-57	9
α-helix	65-83	19
α-helix	85-87	3
α-helix	95-100	6
α-helix	101-104	4
α-helix	111-118	8
α-helix	126-144	19

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gag-Pol polyprotein	C	protein	146	Human immunodeficiency virus type 1	P12497

Sequence of entity 1 (C), FASTA

>4NX4_1 Gag-Pol polyprotein (chains C)
PIVQNLQGQMVHQAISPRTLNAWVKVVEEKAFSPEVIPMFSALSEGATPQDLNTMLNTVG
GHQAAMQMLKETINEEAAEWDRLHPVHAGPIAPGQMREPRGSDIAGTTSTLQEQIGWMTH
NPPIPVGEIYKRWIILGLNKIVRMYS

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	2
JPR	1-(3-chloro-4-methylphenyl)-3-{2-[({5-[(dimethylamino)methyl]-2-furyl}methyl)th…	C18 H24 Cl N3 O2 S	1

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

Primary citation

Protein structural ensembles are revealed by redefining X-ray electron density noise. Lang, P.T., Holton, J.M., Fraser, J.S. et al. Proc Natl Acad Sci U S A (2014) 111:237-242. DOI 10.1073/pnas.1302823110 · 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)
2XDE 1.4 Å, Crystal structure of the complex of PF-3450074 with an engineered HIV capsid N terminal…
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
6MCS 1.52 Å, X-ray crystal structure of wild type HIV-1 protease in complex with GRL-003

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