4EJK: Protease

HIV Protease (PR) dimer in closed form with pepstatin in active site and fragment 1F1-N in the outside/top of flap. Determined by X-ray diffraction at 1.79 Å resolution. Released 1 May 2013.

Method: X-ray diffraction
Resolution: 1.79 Å
Organism: Human immunodeficiency virus 1
Chains: 3
Atoms: 1,711
Mol. weight: 22.54 kDa
Ligands: IOP
Released: 1 May 2013

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

Secondary structure: helices and β-sheets

4EJK 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	32-33	2	2
β-strand	42-47	6	2
β-strand	49	1	3
β-strand	54-66	13	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	4
β-strand	18-24	7	4
β-strand	28	1	5
β-strand	32-33	2	4
β-strand	43-48	6	4
β-strand	53-66	14	4
β-strand	69-77	9	4
β-strand	84-85	2	4
α-helix	87-90	4
α-helix	91-93	3
β-strand	96-98	3	1

Chain N: 0 helices, 2 β-strands

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

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protease	A, B	protein	99	Human immunodeficiency virus 1	P12499
pepstatin	N	protein	6

Sequence of entity 1 (A, B), FASTA

>4EJK_1 Protease (chains A, B)
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYD
QILIEICGHKAIGTVLVGPTPVNIIGRNLLTQIGCTLNF

Sequence of entity 2 (N), FASTA

>4EJK_2 pepstatin (chains N)
XVVXAX

Ligands and cofactors

ID	Name	Formula	Copies
IOP	Indolylpropionic acid	C11 H11 N O2	1

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:

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
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
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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