4EJD: Protease

HIV Protease (PR) dimer in closed form with pepstatin in active site and fragment 1F1 in the outside/top of flap. Determined by X-ray diffraction at 1.1 Å resolution. Released 1 May 2013.

Method: X-ray diffraction
Resolution: 1.1 Å
Organisms: Human immunodeficiency virus 1, Streptomyces argenteolus subsp. toyonakensis
Chains: 3
Atoms: 1,867
Mol. weight: 22.84 kDa
Ligands: 1F1
Released: 1 May 2013

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

Secondary structure: helices and β-sheets

4EJD contains 4 α-helices and 22 β-strands across 3 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: 2 helices, 10 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	28	1	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
α-helix	91-93	3
β-strand	96-98	3	1

Chain B: 2 helices, 10 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	28	1	4
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

Chain C: 0 helices, 2 β-strands

Element	Residues	Length	Sheet
β-strand	3	1	2
β-strand	5	1	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protease	A, B	protein	99	Human immunodeficiency virus 1	P12499
pepstatin	C	protein	6	Streptomyces argenteolus subsp. toyonakensis

Sequence of entity 1 (A, B), FASTA

>4EJD_1 Protease (chains A, B)
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYD
QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Sequence of entity 2 (C), FASTA

>4EJD_2 pepstatin (chains C)
XVVXAX

Ligands and cofactors

ID	Name	Formula	Copies
1F1	1H-indole-6-carboxylic acid	C9 H7 N O2	1

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

Primary citation

Small molecule regulation of protein conformation by binding in the Flap of HIV protease. Tiefenbrunn, T., Forli, S., Baksh, M.M. et al. ACS Chem Biol (2013) 8:1223-1231. DOI 10.1021/cb300611p · PubMed

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

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
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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