4DQB: Wild-type HIV-1 Protease

Crystal Structure of wild-type HIV-1 Protease in Complex with DRV. Determined by X-ray diffraction at 1.5 Å resolution. Released 7 Mar 2012.

Method: X-ray diffraction
Resolution: 1.5 Å
Organism: Human immunodeficiency virus 1
Chains: 2
Atoms: 1,764
Mol. weight: 22.38 kDa
Ligands: 017, PO4
Released: 7 Mar 2012

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

Secondary structure: helices and β-sheets

4DQB 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	31-34	4	2
β-strand	43-49	7	2
β-strand	52-66	15	2
β-strand	69-78	10	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
Aspartyl protease	A, B	protein	99	Human immunodeficiency virus 1	P12499

Sequence of entity 1 (A, B), FASTA

>4DQB_1 Aspartyl protease (chains A, B)
PQITLWKRPLVTIRIGGQLKEALLDTGADDTVIEEMNLPGKWKPKMIGGIGGFIKVRQYD
QIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

Ligands and cofactors

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

Water and common crystallization additives (DMS, EDO) are not listed.

Primary citation

Hydrophobic core flexibility modulates enzyme activity in HIV-1 protease. Mittal, S., Cai, Y., Nalam, M.N. et al. J Am Chem Soc (2012) 134:4163-4168. DOI 10.1021/ja2095766 · PubMed

Other PDB entries of the same protein (UniProt P12499), best resolution first:

4EJD 1.1 Å, HIV Protease (PR) dimer in closed form with pepstatin in active site and fragment 1F1 in…
3KFR 1.3 Å, HIV Protease (PR) dimer with inhibitor TL-3 bound and fragment 1F1 in the outside/top of…
4DQE 1.3 Å, Crystal Structure of (G16C/L38C) HIV-1 Protease in Complex with DRV
4E43 1.54 Å, HIV protease (PR) dimer with acetate in exo site and peptide in active site
5AH7 1.55 Å, Disubstituted bis-THF moieties as new P2 ligands in non-peptidal HIV- 1 Protease…
2WKZ 1.7 Å, HIV-1 Protease Inhibitors Containing a Tertiary Alcohol in the Transition-State Mimic…
3KFN 1.77 Å, HIV Protease (PR) with inhibitor TL-3 and fragment hit 4D9 by soaking
3KFP 1.77 Å, HIV Protease (PR) with inhibitor TL-3 bound, and DMSOs in exo site
4DQH 1.79 Å, Crystal Structure of (R14C/E65C) HIV-1 Protease in complex with DRV
4EJK 1.79 Å, HIV Protease (PR) dimer in closed form with pepstatin in active site and fragment 1F1-N…
1HXW 1.8 Å, HIV-1 protease dimer complexed with a-84538
1PRO 1.8 Å, HIV-1 protease dimer complexed with a-98881

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