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: 22687.60 
• Atom Count: 1647 
• Residue Count: 198 
• Unique protein chains: 1

2FXE

X-ray crystal structure of HIV-1 protease CRM mutant complexed with atazanavir (BMS-232632)

• DOI: 10.2210/pdb2FXE/pdb

• Classification: HYDROLASE
• Organism(s): Human immunodeficiency virus type 1 group M subtype B
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): 9 


• Deposited: 2006-02-05 Released: 2007-02-20 
• Deposition Author(s): Sheriff, S., Klei, H.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.202 
• R-Value Work: 0.169 

Literature

X-ray crystal structures of human immunodeficiency virus type 1 protease mutants complexed with atazanavir.

Klei, H.E., Kish, K., Lin, P.F., Guo, Q., Friborg, J., Rose, R.E., Zhang, Y., Goldfarb, V., Langley, D.R., Wittekind, M., Sheriff, S.

(2007) J.Virol. 81: 9525-9535

• PubMed: 17537865 
• DOI: 10.1128/JVI.02503-05
• Primary Citation of Related Structures:  
  2FXD


• PubMed Abstract: 
  

Atazanavir, which is marketed as REYATAZ, is the first human immunodeficiency virus type 1 (HIV-1) protease inhibitor approved for once-daily administration. As previously reported, atazanavir offers improved inhibitory profiles against several common variants of HIV-1 protease over those of the other peptidomimetic inhibitors currently on the market. This work describes the X-ray crystal structures of complexes of atazanavir with two HIV-1 protease variants, namely, (i) an enzyme optimized for resistance to autolysis and oxidation, referred to as the cleavage-resistant mutant (CRM); and (ii) the M46I/V82F/I84V/L90M mutant of the CRM enzyme, which is resistant to all approved HIV-1 protease inhibitors, referred to as the inhibitor-resistant mutant. In these two complexes, atazanavir adopts distinct bound conformations in response to the V82F substitution, which may explain why this substitution, at least in isolation, has yet to be selected in vitro or in the clinic. Because of its nearly symmetrical chemical structure, atazanavir is able to make several analogous contacts with each monomer of the biological dimer.

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Organizational Affiliation: 

Macromolecular Crystallography, Bristol-Myers Squibb Pharmaceutical Research Institute, Princeton, NJ 08543-4000, USA. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
pol protein	A, B	99	Human immunodeficiency virus type 1 group M subtype B	Mutation(s): 9  Gene Names: gag-pol
Find proteins for P05959 (Human immunodeficiency virus type 1 group M subtype B) Go to UniProtKB:  P05959

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
SO4	A, B	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
ACT	A	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
GOL	A, B	GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DR7	A	(3S,8S,9S,12S)-3,12-BIS(1,1-DIMETHYLETHYL)-8-HYDROXY-4,11-DIOXO-9-(PHENYLMETHYL)-6-[[4-(2-PYRIDINYL)PHENYL]METHYL]-2,5,6,10,13-PENTAAZATETRADECANEDIOIC ACID DIMETHYL ESTER ATAZANAVIR; METHYL [(1S,4S,5S,10S)-4-BENZYL-1,10-DI-TERT-BUTYL-5-HYDROXY-2,9,12-TRIOXO-7-(4-PYRIDIN-2-YLBENZYL)-13-OXA-3,7,8,11-TETRAAZATETRADEC-1-YL]CARBAMATE C38 H52 N6 O7 AXRYRYVKAWYZBR-GASGPIRDSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DR7	IC50: 0 nM (89) BINDINGDB
DR7	Ki: 0 - 1.1 nM (90) BINDINGDB
DR7	Kd: 0.4 nM (89) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.8 Å
• R-Value Free: 0.202 
• R-Value Work: 0.169 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 51.186	α = 90.00
b = 58.207	β = 90.00
c = 61.285	γ = 90.00

Software Package:

Software Name	Purpose
HKL-2000	data reduction
AMoRE	phasing
CNX	refinement
HKL-2000	data scaling
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-02-05 
• Released Date: 2007-02-20 
• Deposition Author(s): Sheriff, S., Klei, H.E.

Revision History 

• Version 1.0: 2007-02-20
  Type: Initial release
• Version 1.1: 2008-05-01
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance