Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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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: 22202.20 
• Atom Count: 1565 
• Residue Count: 198 
• Unique protein chains: 1

1ODY

HIV-1 PROTEASE COMPLEXED WITH AN INHIBITOR LP-130

• DOI: 10.2210/pdb1ODY/pdb

• Classification: ASPARTIC PROTEASE
• Organism(s): Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)
• Expression System: Escherichia coli


• Deposited: 1998-07-13 Released: 1999-02-16 
• Deposition Author(s): Kervinen, J., Lubkowski, J., Zdanov, A., Wlodawer, A., Gustchina, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Work: 0.167 

Literature

Toward a universal inhibitor of retroviral proteases: comparative analysis of the interactions of LP-130 complexed with proteases from HIV-1, FIV, and EIAV.

Kervinen, J., Lubkowski, J., Zdanov, A., Bhatt, D., Dunn, B.M., Hui, K.Y., Powell, D.J., Kay, J., Wlodawer, A., Gustchina, A.

(1998) Protein Sci. 7: 2314-2323

• PubMed: 9827997 
• DOI: 10.1002/pro.5560071108
• Primary Citation of Related Structures:  
  4FIV, 2FMB


• PubMed Abstract: 
  

One of the major problems encountered in antiviral therapy against AIDS is the emergence of viral variants that exhibit drug resistance. The sequences of proteases (PRs) from related retroviruses sometimes include, at structurally equivalent positions, amino acids identical to those found in drug-resistant forms of HIV-1 PR. The statine-based inhibitor LP-130 was found to be a universal, nanomolar-range inhibitor against all tested retroviral PRs. We solved the crystal structures of LP-130 in complex with retroviral PRs from HIV-1, feline immunodeficiency virus, and equine infectious anemia virus and compared the structures to determine the differences in the interactions between the inhibitor and the active-site residues of the enzymes. This comparison shows an extraordinary similarity in the binding modes of the inhibitor molecules. The only exceptions are the different conformations of naphthylalanine side chains at the P3/P3' positions, which might be responsible for the variation in the Ki values. These findings indicate that successful inhibition of different retroviral PRs by LP-130 is achieved because this compound can be accommodated without serious conformational differences, despite the variations in the type of residues forming the active-site region. Although strong, specific interactions between the ligand and the enzyme might improve the potency of the inhibitor, the absence of such interactions seems to favor the universality of the compound. Hence, the ability of potential anti-AIDS drugs to inhibit multiple retroviral PRs might indicate their likelihood of not eliciting drug resistance. These studies may also contribute to the development of a small-animal model for preclinical testing of antiviral compounds.

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Organizational Affiliation: 

Macromolecular Structure Laboratory, ABL-Basic Research Program, NCI-Frederick Cancer Research and Development Center, Maryland 21702, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
HIV-1 PROTEASE	A, B	99	Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)	Mutation(s): 0  Gene Names: gag-pol
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Go to UniProtKB:  P04585

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
LP1	A	4-[2-(2-ACETYLAMINO-3-NAPHTALEN-1-YL-PROPIONYLAMINO)-4-METHYL-PENTANOYLAMINO]-3-HYDROXY-6-METHYL-HEPTANOIC ACID [1-(1-CARBAMOYL-2-NAPHTHALEN-1-YL-ETHYLCARBAMOYL)-PROPYL]-AMIDE C45 H58 N6 O7 ACPDNLLISIAERE-ZYWZKTPASA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
LP1	Ki: 8 nM BINDINGMOAD
LP1	Ki: 8 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2 Å
• R-Value Work: 0.167 
• Space Group: P 6₁

Unit Cell:

Length (Å)	Angle (°)
a = 62.900	α = 90.00
b = 62.900	β = 90.00
c = 83.310	γ = 120.00

Software Package:

Software Name	Purpose
DENZO	data reduction
X-PLOR	refinement
X-PLOR	phasing
X-PLOR	model building
PROFFT	refinement
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-07-13 
• Released Date: 1999-02-16 
• Deposition Author(s): Kervinen, J., Lubkowski, J., Zdanov, A., Wlodawer, A., Gustchina, A.

Revision History 

• Version 1.0: 1999-02-16
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance