4Q1Y: Aspartyl protease

Mutations Outside the Active Site of HIV-1 Protease Alter Enzyme Structure and Dynamic Ensemble of the Active Site to Confer Drug Resistance. Determined by X-ray diffraction at 1.5 Å resolution. Released 18 Feb 2015.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Human immunodeficiency virus 1
Chains: 2
Atoms: 1,761
Mol. weight: 22.74 kDa
Ligands: PO4, 017
Released: 18 Feb 2015

Explore 4Q1Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4Q1Y 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	31-33	3	2
β-strand	43-49	7	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	10-14	5	3
β-strand	19-24	6	3
β-strand	31-33	3	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
aspartyl protease	A, B	protein	99	Human immunodeficiency virus 1	P04585 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4Q1Y_1 aspartyl protease (chains A, B)
PQITLWKRPLVTIRIGGQLKEALLDTGADDTIFEEMNLPGKWKPKMIGGIGGFIKVRQYD
QIPIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligands and cofactors

ID	Name	Formula	Copies
PO4	Phosphate ion	O4 P	3
017	(3R,3AS,6AR)-HEXAHYDROFURO[2,3-b]furan-3-YL(1S,2R)-3-[[(4-aminophenyl)sulfonyl]…	C27 H37 N3 O7 S	1

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

Primary citation

Drug resistance conferred by mutations outside the active site through alterations in the dynamic and structural ensemble of HIV-1 protease. Ragland, D.A., Nalivaika, E.A., Nalam, M.N. et al. J Am Chem Soc (2014) 136:11956-11963. DOI 10.1021/ja504096m · PubMed

Other PDB entries of the same protein (UniProt P04585 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6DV4 1.14 Å, HIV-1 wild type protease with GRL-04315A, a tetrahydronaphthalene carboxamide with…
6DIF 1.2 Å, Wild-type HIV-1 protease in complex with tipranavir
6DV0 1.2 Å, HIV-1 wild type protease with GRL-02815A, a thiochroman heterocycle with (S)-Boc-amine…
5DGU 1.22 Å, Crystal Structure of HIV-1 Protease Inhibitors Containing Substituted…
6E9A 1.22 Å, HIV-1 wild type protease with grl-034-17A, (3aS, 5R, 6aR)-2-oxohexahyd…
6DJ1 1.26 Å, Wild-type HIV-1 protease in complex with Lopinavir
8F0F 1.29 Å, HIV-1 wild type protease with GRL-110-19A, a chloroacetamide derivative based on…
6E7J 1.3 Å, HIV-1 wild type protease with GRL-042-17A, 3-phenylhexahydro-2h-cyclopenta[d]oxazol-2-one…
6DJ7 1.31 Å, HIV-1 protease with mutation L76V in complex with GRL-5010…
8ESX 1.35 Å, HIV protease in complex with benzoxaborolone analog of darunavir
8ESY 1.35 Å, D30N mutant HIV protease in complex with benzoxaborolone analog of darunavir
6DJ2 1.36 Å, HIV-1 protease with single mutation L76V in complex with Lopinavir

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