Biological Assembly 1  

 3D View: Structure | Electron Density | Validation Report | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 22.34 kDa 
• Atom Count: 1765 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

1ZSF

Crystal Structure of Complex of a Hydroxyethylamine Inhibitor with HIV-1 Protease at 2.0A Resolution

• DOI: 10.2210/pdb1ZSF/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-05-24 Released: 2006-04-25 
• Deposition Author(s): Duskova, J., Skalova, T., Dohnalek, J., Petrokova, H., Hasek, J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.276 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 

Literature

On the role of the R configuration of the reaction-intermediate isostere in HIV-1 protease-inhibitor binding: X-ray structure at 2.0 A resolution.

Duskova, J., Dohnalek, J., Skalova, T., Petrokova, H., Vondrackova, E., Hradilek, M., Konvalinka, J., Soucek, M., Brynda, J., Fabry, M., Sedlacek, J., Hasek, J.

(2006) Acta Crystallogr D Biol Crystallogr 62: 489-497

• PubMed: 16627941 
• DOI: 10.1107/S0907444906006718
• Primary Citation of Related Structures:  
  1ZSF, 1ZSR


• PubMed Abstract: 
  

Peptidomimetic inhibitors of human immunodeficiency virus-1 protease are successful lead substances for the development of virostatic drugs against HIV as the causative agent of acquired immunodeficiency syndrome (AIDS). The hydroxyethylamine isostere of the proteolytic cleavage intermediate provides a suitable replacement for the peptide bond. A series of acyclic pseudopeptide inhibitors with the hydroxyethylamine isostere varying in chiral carbon configuration and P'2 residue type were structurally analysed by single-crystal X-ray crystallography. The compounds inhibit HIV protease with subnanomolar inhibition constants and block viral replication in tissue cultures. Here, the structure of such a complex with the R configuration of the isosteric group (PDB code 1zsf) is presented together with newly available synchrotron data for a complex with the S stereoisomer of the inhibitor (PDB code 1zsr). Comparison of the structure and binding with other complexes of HIV-1 protease and similar inhibitors contributes to the understanding of how these molecules bind to the wild-type form of this enzyme. The hydroxy group of the R stereoisomer interacts with one of the catalytic aspartic acids by a short hydrogen bond with rather extreme geometry. The change of configuration of the chiral carbon bearing the hydroxyl from S to R does not influence the inhibition efficiency in this case.

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Organizational Affiliation: 

Institute of Macromolecular Chemistry, Academy of Sciences of the Czech Republic, Heyrovského nám. 2, 162 06 Praha 6, Czech Republic. [e-mail]

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASE RETROPEPSIN	A, B	99	Human immunodeficiency virus 1	Mutation(s): 0  EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
UniProt
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10)) Explore P03366  Go to UniProtKB:  P03366

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
0ZS (Subject of Investigation/LOI)	C [auth B]	N-{(2R,3S)-3-[(tert-butoxycarbonyl)amino]-2-hydroxy-4-phenylbutyl}-L-phenylalanyl-L-alpha-glutamyl-L-phenylalaninamide C38 H49 N5 O8 MPMUDVMRFYJRLP-QEUNAIBPSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	A, B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Binding Affinity Annotations
ID	Source	Binding Affinity
0ZS	Binding MOAD:  1ZSF	Ki: 0.12 (nM) from 1 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000385 (0ZS)	C [auth B]	BOC-PHE-PSI[R-CH(OH)CH2NH]-PHE-GLU-PHE-NH2	Peptide-like / Inhibitor		Ligand Interaction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.98 Å
• R-Value Free: 0.276 
• R-Value Work: 0.221 
• R-Value Observed: 0.222 
• Space Group: P 6₁
• Diffraction Data DOI: 10.15785/SBGRID/729 SBGrid

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.864	α = 90
b = 62.864	β = 90
c = 82.375	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
SHELXL-97	refinement

Structure Validation

Ligand Structure Quality Assessment  

Entry History 

Deposition Data

• Deposited Date: 2005-05-24 
• Released Date: 2006-04-25 
Deposition Author(s): Duskova, J., Skalova, T., Dohnalek, J., Petrokova, H., Hasek, J.

Revision History  

• Version 1.0: 2006-04-25
  Type: Initial release
  
• Version 1.1: 2007-10-16
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2012-12-12
  Changes: Other