Biological Assembly 1  

 3D View: Structure | 1D-3D View | 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: 22.20 kDa 
• Atom Count: 1710 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

1ODY

HIV-1 PROTEASE COMPLEXED WITH AN INHIBITOR LP-130

• PDB DOI: 10.2210/pdb1ODY/pdb

• Classification: ASPARTIC PROTEASE
• Organism(s): HIV-1 M:B_HXB2R
• Expression System: Escherichia coli
• Mutation(s): No 


• 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: 2.00 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:  
  1ODY, 2FMB, 4FIV


• 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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 PROTEASE	A, B	99	HIV-1 M:B_HXB2R	Mutation(s): 0  Gene Names: gag-pol 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 P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
LP1	C [auth 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

Binding Affinity Annotations
ID	Source	Binding Affinity
LP1	Binding MOAD:  1ODY	Ki: 8 (nM) from 1 assay(s)
	PDBBind:  1ODY	Ki: 8 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Work: 0.167 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.9	α = 90
b = 62.9	β = 90
c = 83.31	γ = 120

Software Package:

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

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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance