8ESY: D30N mutant HIV protease

D30N mutant HIV protease in complex with benzoxaborolone analog of darunavir. Determined by X-ray diffraction at 1.35 Å resolution. Released 8 Feb 2023.

Method: X-ray diffraction
Resolution: 1.35 Å
Organism: Human immunodeficiency virus 1
Chains: 2
Atoms: 1,878
Mol. weight: 22.3 kDa
Ligands: X7B
Released: 8 Feb 2023

Explore 8ESY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8ESY 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	20-24	5	2
β-strand	31-33	3	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	102-103	2	1
β-strand	110-115	6	3
β-strand	118-124	7	3
β-strand	132-133	2	3
β-strand	143-149	7	3
β-strand	152-166	15	3
β-strand	169-177	9	3
β-strand	184-185	2	3
α-helix	187-192	6
β-strand	196-198	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protease	A, B	protein	99	Human immunodeficiency virus 1	P04585 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>8ESY_1 Protease (chains A, B)
PQITLWKRPLVTIKIGGQLKEALLDTGADNTVIEEMSLPGRWKPKMIGGIGGFIKVRQYD
QIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

Ligands and cofactors

ID	Name	Formula	Copies
X7B	[(3~{a}~{S},4~{R},6~{a}~{R})-2,3,3~{a},4,5,6~{a}-hexahydrofuro[2,3-b]furan-4-yl…	C28 H36 B N2 O11 S	1

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

Primary citation

Inhibition of HIV-1 Protease by a Boronic Acid with High Oxidative Stability. Graham, B.J., Windsor, I.W., Raines, R.T. ACS Med Chem Lett (2023) 14:171-175. DOI 10.1021/acsmedchemlett.2c00464 · 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
6DJ2 1.36 Å, HIV-1 protease with single mutation L76V in complex with Lopinavir
4U1J 1.38 Å, HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential…

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