5YOK: HIV-1 Protease

Structure of HIV-1 Protease in Complex with Inhibitor KNI-1657. Determined by X-ray diffraction at 0.85 Å resolution. Released 18 Jul 2018.

Method: X-ray diffraction
Resolution: 0.85 Å
Organism: Human immunodeficiency virus 1
Chains: 2
Atoms: 2,395
Mol. weight: 22.68 kDa
Ligands: 8Z0
Released: 18 Jul 2018

Explore 5YOK in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5YOK contains 2 α-helices and 18 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: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	1
β-strand	10-15	6	2
β-strand	18-24	7	2
β-strand	32-33	2	2
β-strand	42-49	8	2
β-strand	52-66	15	2
β-strand	69-77	9	2
β-strand	84-85	2	2
α-helix	87-90	4
β-strand	96-98	3	1

Chain B: 1 helix, 9 β-strands

Element	Residues	Length	Sheet
β-strand	2-3	2	1
β-strand	10-15	6	3
β-strand	18-24	7	3
β-strand	32-33	2	3
β-strand	43-49	7	3
β-strand	52-66	15	3
β-strand	69-77	9	3
β-strand	84-85	2	3
α-helix	87-90	4
β-strand	96-98	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
HIV-1 protease	A, B	protein	100	Human immunodeficiency virus 1	P03367

Sequence of entity 1 (A, B), FASTA

>5YOK_1 HIV-1 PROTEASE (chains A, B)
MPQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFIKVRQY
DQIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

Ligands and cofactors

ID	Name	Formula	Copies
8Z0	(4R)-N-[(2,6-dimethylphenyl)methyl]-3-[(2S,3S)-3-[[(2S)-2-[(7-methoxy-1-benzofu…	C41 H48 N4 O8 S	1

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

Primary citation

Identification of Highly Potent Human Immunodeficiency Virus Type-1 Protease Inhibitors against Lopinavir and Darunavir Resistant Viruses from Allophenylnorstatine-Based Peptidomimetics with P2 Tetrahydrofuranylglycine. Hidaka, K., Kimura, T., Sankaranarayanan, R. et al. J Med Chem (2018) 61:5138-5153. DOI 10.1021/acs.jmedchem.7b01709 · PubMed

Other PDB entries of the same protein (UniProt P03367), best resolution first:

3A2O 0.88 Å, Crystal Structure of HIV-1 Protease Complexed with KNI-1689
3FX5 0.93 Å, Structure of HIV-1 Protease in Complex with Potent Inhibitor KNI-272 Determined by High…
3DJK 1.0 Å, Wild Type HIV-1 Protease with potent Antiviral inhibitor GRL-0255A
1NH0 1.03 Å, 1.03 A structure of HIV-1 protease: inhibitor binding inside and outside the active site
3NDX 1.03 Å, HIV-1 Protease Saquinavir:Ritonavir 1:50 complex structure
3BVA 1.05 Å, Cystal structure of HIV-1 Active Site Mutant D25N and p2-NC analog inhibitor
4HE9 1.06 Å, Crystal Structure of HIV-1 protease mutants I54M complexed with inhibitor GRL-0519
3DK1 1.07 Å, Wild Type HIV-1 Protease with potent Antiviral inhibitor GRL-0105A
2QD7 1.11 Å, HIV-1 Protease Mutant V82A with potent Antiviral inhibitor GRL-98065
3TOH 1.12 Å, HIV-1 Protease - Epoxydic Inhibitor Complex (pH 9 - Orthorombic Crystal form P212121)
8FUJ 1.12 Å, HIV-1 wild type protease with GRL-03419A, with N-(2,5-dimethylphenyl)-4-(pyridin-3-yl)pyr…
7TO5 1.13 Å, HIV-1 wild type protease with GRL-05816A, with C-4 substituted cyclohexane-fused…

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