2WKZ: Protease

HIV-1 Protease Inhibitors Containing a Tertiary Alcohol in the Transition-State Mimic with Improved Cell-Based Antiviral Activity. Determined by X-ray diffraction at 1.7 Å resolution. Released 15 Dec 2009.

Method: X-ray diffraction
Resolution: 1.7 Å
Organism: HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (Z2/CDC-Z34 ISOLATE)
Chains: 2
Atoms: 1,737
Mol. weight: 22.3 kDa
Ligands: 5AH
Released: 15 Dec 2009

Explore 2WKZ in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2WKZ 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	32-33	2	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	187-190	4
β-strand	196-198	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protease	A, B	protein	99	HUMAN IMMUNODEFICIENCY VIRUS TYPE 1 (Z2/CDC-Z34 ISOLATE)	P12499

Sequence of entity 1 (A, B), FASTA

>2WKZ_1 PROTEASE (chains A, B)
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMSLPGRWKPKMIGGIGGFIKVRQYD
QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligands and cofactors

ID	Name	Formula	Copies
5AH	Methyl [(1S)-1-({2-[(3S)-3-benzyl-3-hydroxy-4-{[(1S,2R)-2-hydroxy-2,3-dihydro-1…	C40 H47 N5 O6	1

Primary citation

HIV-1 Protease Inhibitors with a Transition-State Mimic Comprising a Tertiary Alcohol: Improved Antiviral Activity in Cells. Mahalingam, A.K., Axelsson, L., Ekegren, J.K. et al. J Med Chem (2010) 53:607. DOI 10.1021/JM901165G · 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
4DQB 1.5 Å, Crystal Structure of wild-type 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…
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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