3KFP: Protease

HIV Protease (PR) with inhibitor TL-3 bound, and DMSOs in exo site. Determined by X-ray diffraction at 1.77 Å resolution. Released 23 Feb 2010.

Method: X-ray diffraction
Resolution: 1.77 Å
Organism: Human immunodeficiency virus 1
Chains: 1
Atoms: 908
Mol. weight: 12.05 kDa
Ligands: 3TL
Released: 23 Feb 2010

Explore 3KFP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3KFP contains 1 α-helix and 7 β-strands across 1 chain. 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, 7 β-strands

Element	Residues	Length	Sheet
β-strand	10-15	6	1
β-strand	18-24	7	1
β-strand	32-33	2	1
β-strand	43-49	7	1
β-strand	52-66	15	1
β-strand	69-77	9	1
β-strand	84-85	2	1
α-helix	87-90	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protease	A	protein	99	Human immunodeficiency virus 1	P12499

Sequence of entity 1 (A), FASTA

>3KFP_1 Protease (chains A)
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYD
QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Ligands and cofactors

ID	Name	Formula	Copies
3TL	benzyl [(1S,4S,7S,8R,9R,10S,13S,16S)-7,10-dibenzyl-8,9-dihydroxy-1,16-dimethyl-…	C50 H64 N6 O10	1

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

Primary citation

Fragment-based screen against HIV protease. Perryman, A.L., Zhang, Q., Soutter, H.H. et al. Chem Biol Drug Des (2010) 75:257-268. DOI 10.1111/j.1747-0285.2009.00943.x · 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…
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
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

Browse structure collections

About this viewer

MolViewer shows 3KFP directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.