3DK1: Protease

Wild Type HIV-1 Protease with potent Antiviral inhibitor GRL-0105A. Determined by X-ray diffraction at 1.07 Å resolution. Released 12 May 2009.

Method: X-ray diffraction
Resolution: 1.07 Å
Organism: Human immunodeficiency virus type 1
Chains: 2
Atoms: 1,955
Mol. weight: 22.19 kDa
Ligands: G05
Released: 12 May 2009

Explore 3DK1 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3DK1 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	2-4	3	1
β-strand	10-15	6	2
β-strand	18-24	7	2
β-strand	31-33	3	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	P03367

Sequence of entity 1 (A, B), FASTA

>3DK1_1 Protease (chains A, B)
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVIEEMSLPGRWKPKMIGGIGGFIKVRQYD
QIIIEIAGHKAIGTVLVGPTPVNIIGRNLLTQIGATLNF

Ligands and cofactors

ID	Name	Formula	Copies
G05	(4aR,6r,7aS)-hexahydro-4aH-cyclopenta[b][1,4]dioxin-6-yl…	C29 H40 N2 O8 S	1

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

Primary citation

Potent HIV-1 protease inhibitors incorporating meso-bicyclic urethanes as P2-ligands: structure-based design, synthesis, biological evaluation and protein-ligand X-ray studies. Ghosh, A.K., Gemma, S., Takayama, J. et al. Org Biomol Chem (2008) 6:3703-3713. DOI 10.1039/b809178a · PubMed

Other PDB entries of the same protein (UniProt P03367), best resolution first:

5YOK 0.85 Å, Structure of HIV-1 Protease in Complex with Inhibitor KNI-1657
3A2O 0.88 Å, Crystal Structure of HIV-1 Protease Complexed with KNI-1689
3FX5 0.93 Å, Structure of HIV-1 Protease in Complex with Potent Inhibitor KNI-272 Determined by High…
3DJK 1.0 Å, Wild Type HIV-1 Protease with potent Antiviral inhibitor GRL-0255A
1NH0 1.03 Å, 1.03 A structure of HIV-1 protease: inhibitor binding inside and outside the active site
3NDX 1.03 Å, HIV-1 Protease Saquinavir:Ritonavir 1:50 complex structure
3BVA 1.05 Å, Cystal structure of HIV-1 Active Site Mutant D25N and p2-NC analog inhibitor
4HE9 1.06 Å, Crystal Structure of HIV-1 protease mutants I54M complexed with inhibitor GRL-0519
2QD7 1.11 Å, HIV-1 Protease Mutant V82A with potent Antiviral inhibitor GRL-98065
3TOH 1.12 Å, HIV-1 Protease - Epoxydic Inhibitor Complex (pH 9 - Orthorombic Crystal form P212121)
8FUJ 1.12 Å, HIV-1 wild type protease with GRL-03419A, with N-(2,5-dimethylphenyl)-4-(pyridin-3-yl)pyr…
7TO5 1.13 Å, HIV-1 wild type protease with GRL-05816A, with C-4 substituted cyclohexane-fused…

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