3WNH: Cyclic hexapeptide PKZDNv

Cyclic hexapeptide PKZDNv in complex with HIV-1 integrase. Determined by X-ray diffraction at 1.5 Å resolution. Released 25 Dec 2013.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Human immunodeficiency virus type 1
Chains: 4
Atoms: 2,480
Mol. weight: 36.67 kDa
Ligands: CD
Released: 25 Dec 2013

Explore 3WNH in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3WNH contains 14 α-helices and 10 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: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	60-68	9	1
β-strand	71-78	8	1
β-strand	84-89	6	1
α-helix	94-107	14
β-strand	112-114	3	1
α-helix	119-121	3
α-helix	125-133	9
β-strand	136	1	1
α-helix	153-165	13
α-helix	166-168	3
α-helix	172-185	14
α-helix	196-208	13

Chain B: 7 helices, 5 β-strands

Element	Residues	Length	Sheet
β-strand	60-68	9	2
β-strand	71-78	8	2
β-strand	84-89	6	2
α-helix	94-107	14
β-strand	112-114	3	2
α-helix	119-121	3
α-helix	125-133	9
β-strand	136-137	2	2
α-helix	154-165	12
α-helix	166-168	3
α-helix	172-185	14
α-helix	196-208	13

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Gag-Pol polyprotein	A, B	protein	157	Human immunodeficiency virus type 1	P12497
PK(NLE)DN(DVA) peptide	C, D	protein	6

Sequence of entity 1 (A, B), FASTA

>3WNH_1 Gag-Pol polyprotein (chains A, B)
SSPGIWQLDCTHLEGKVILVAVHVASGYIEAEVIPAETGQETAYFLLKLAGRWPVKTVHT
DNGSNFTGATVRAACDWAGIKQEDGIPYNPQSQGVIESMNKELKKIIGQVRDQAEHLKTA
VQMAVFIHNHKRKGGIGGYSAGERIVDIIATDIQTKE

Sequence of entity 2 (C, D), FASTA

>3WNH_2 PK(NLE)DN(DVA) peptide (chains C, D)
PKLDNV

Ligands and cofactors

ID	Name	Formula	Copies
CD	Cadmium ion	Cd	4

Water and common crystallization additives (SO4, CL) are not listed.

Primary citation

Hexapeptide mimetics of LEDGF in complex with HIV-1 integrase. Northfield, S.E., Wielens, J., Headey, S.J. et al. To be published.

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
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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