6DJ7: HIV-1 protease with mutation L76V

HIV-1 protease with mutation L76V in complex with GRL-5010 (gem-difluoro-bis-tetrahydrofuran as P2 ligand). Determined by X-ray diffraction at 1.31 Å resolution. Released 17 Oct 2018.

Method: X-ray diffraction
Resolution: 1.31 Å
Organism: Human immunodeficiency virus 1
Chains: 2
Atoms: 2,042
Mol. weight: 22.47 kDa
Ligands: G10
Released: 17 Oct 2018

Explore 6DJ7 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6DJ7 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	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	31-33	3	3
β-strand	43-47	5	3
β-strand	54-66	13	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	99	Human immunodeficiency virus 1	P04585 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6DJ7_1 HIV-1 protease (chains A, B)
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFIKVRQYD
QIIIEIAGHKAIGTVVVGPTPVNIIGRNLLTQIGATLNF

Ligands and cofactors

ID	Name	Formula	Copies
G10	(3R,3aS,6aS)-4,4-difluorohexahydrofuro[2,3-b]furan-3-yl…	C27 H35 F2 N3 O7 S	1

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

Primary citation

Drug Resistance Mutation L76V Alters Nonpolar Interactions at the Flap-Core Interface of HIV-1 Protease. Wong-Sam, A., Wang, Y.F., Zhang, Y. et al. ACS Omega (2018) 3:12132-12140. DOI 10.1021/acsomega.8b01683 · 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…
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
4U1J 1.38 Å, HLA class I micropolymorphisms determine peptide-HLA landscape and dictate differential…

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