3EC0: High Resolution HIV-2 Protease Structure

High Resolution HIV-2 Protease Structure in Complex with Antiviral Inhibitor GRL-06579A. Determined by X-ray diffraction at 1.18 Å resolution. Released 16 Sept 2008.

Method: X-ray diffraction
Resolution: 1.18 Å
Organism: Human immunodeficiency virus type 2 (ISOLATE ROD)
Chains: 2
Atoms: 1,846
Mol. weight: 23.39 kDa
Ligands: ZN, GRL
Released: 16 Sept 2008

Explore 3EC0 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3EC0 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	43-49	7	2
β-strand	52-66	15	2
β-strand	69-78	10	2
β-strand	84-85	2	2
α-helix	87-93	7
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	187-193	7
β-strand	196-198	3	1

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Protease	A, B	protein	99	Human immunodeficiency virus type 2 (ISOLATE ROD)	P04584

Sequence of entity 1 (A, B), FASTA

>3EC0_1 Protease (chains A, B)
PQFSLWKRPVVTAYIEGQPVEVLLDTGADDSIVAGIELGNNYSPKIVGGIGGFINTKEYK
NVEIEVLNKKVRATIMTGDTPINIFGRNILTALGMSLNL

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	10
GRL	(3AS,5R,6AR)-hexahydro-2H-cyclopenta[b]furan-5-yl…	C29 H40 N2 O7 S	1

Water and common crystallization additives (IMD, NA, CL) are not listed.

Primary citation

Structural evidence for effectiveness of darunavir and two related antiviral inhibitors against HIV-2 protease. Kovalevsky, A.Y., Louis, J.M., Aniana, A. et al. J Mol Biol (2008) 384:178-192. DOI 10.1016/j.jmb.2008.09.031 · PubMed

Other PDB entries of the same protein (UniProt P04584), best resolution first:

3ECG 1.18 Å, High Resolution HIV-2 Protease Structure in Complex with Antiviral Inhibitor GRL-98065
3EBZ 1.2 Å, High Resolution HIV-2 Protease Structure in Complex with Clinical Drug Darunavir
1IDA 1.7 Å, Crystal structures of HIV-2 protease in complex with inhibitors containing the…
1HSH 1.9 Å, Crystal structure at 1.9 Å resolution of human immunodeficiency virus (HIV) II protease…
4UPJ 1.9 Å, Human immunodeficiency virus type 2 protease mutant with lys 57 replaced by leu (K57L)…
2HPE 2.0 Å, Comparison of the structures of HIV-2 protease complexes in three crystal space groups…
1IDB 2.2 Å, Crystal structures of HIV-2 protease in complex with inhibitors containing the…
2MIP 2.2 Å, Crystal structure of human immunodeficiency virus (HIV) type 2 protease in complex with…
1HII 2.3 Å, Comparative analysis of the X-ray structures of HIV-1 and HIV-2 proteases in complex…
5UPJ 2.3 Å, HIV-2 PROTEASE/U99283 complex
6UPJ 2.34 Å, HIV-2 PROTEASE/U99294 complex
1MU2 2.35 Å, Crystal structure of HIV-2 reverse transcriptase

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