6PRF: Protease

HIV-1 Protease multiple drug resistant clinical isolate mutant PR20 with GRL-14213A. Determined by X-ray diffraction at 1.21 Å resolution. Released 18 Sept 2019.

Method: X-ray diffraction
Resolution: 1.21 Å
Organism: Human immunodeficiency virus type 1 group M subtype
Chains: 2
Atoms: 2,151
Mol. weight: 23.04 kDa
Ligands: 7OA, Y1
Released: 18 Sept 2019

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

Secondary structure: helices and β-sheets

6PRF contains 3 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	43-49	7	2
β-strand	52-66	15	2
β-strand	69-77	9	2
β-strand	84-85	2	2
α-helix	87-92	6
β-strand	96-98	3	1

Chain B: 2 helices, 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
α-helix	91-93	3
β-strand	96-98	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protease	A, B	protein	99	Human immunodeficiency virus type 1 group M subtype	P03366

Sequence of entity 1 (A, B), FASTA

>6PRF_1 Protease (chains A, B)
PQITLWKRPFVTVKVGGQLKEALLDTGADNTIFEDINLPGRWKPKMVGGIGGFLKVREYD
QVPIEIAGHKVIGTVLVGPTPVNVIGRDTMTQIGATLNF

Ligands and cofactors

ID	Name	Formula	Copies
7OA	(3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl…	C33 H40 F2 N4 O7 S2	1
Y1	Yttrium ion	Y	9

Primary citation

Potent antiviral HIV-1 protease inhibitor combats highly drug resistant mutant PR20. Kneller, D.W., Agniswamy, J., Ghosh, A.K. et al. Biochem Biophys Res Commun (2019) 519:61-66. DOI 10.1016/j.bbrc.2019.08.126 · PubMed

Other PDB entries of the same protein (UniProt P03366), best resolution first:

2HS1 0.84 Å, Ultra-high resolution X-ray crystal structure of HIV-1 protease V32I mutant with TMC114…
3NU3 1.02 Å, Wild Type HIV-1 Protease with Antiviral Drug Amprenavir
2IDW 1.1 Å, Crystal structure analysis of HIV-1 protease mutant V82A with a potent non-peptide…
4ZIP 1.11 Å, HIV-1 wild Type protease with GRL-0648A (a isophthalamide-derived P2-Ligand)
3NU6 1.16 Å, Crystal Structure of HIV-1 Protease Mutant I54M with Antiviral Drug Amprenavir
5JG1 1.16 Å, HIV-1 wild Type protease with GRL-031-14A (a Adamantane P1-Ligand with…
3NU4 1.2 Å, Crystal Structure of HIV-1 Protease Mutant V32I with Antiviral Drug Amprenavir
5AGZ 1.2 Å, Disubstituted bis-THF moieties as new P2 ligands in non-peptidal HIV- 1 Protease…
2HS2 1.22 Å, Crystal structure of M46L mutant of HIV-1 protease complexed with TMC114 (darunavir)
5AH8 1.26 Å, Disubstituted bis-THF moieties as new P2 ligands in non-peptidal HIV- 1 Protease…
3OK9 1.27 Å, Crystal structure of wild-type HIV-1 protease with new oxatricyclic designed inhibitor…
5UPZ 1.27 Å, HIV-1 wild Type protease with GRL-0518A , an isophthalamide-derived P2-P3 ligand with…

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