Biological Assembly 1  

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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: 21901.95 
• Atom Count: 1540 
• Residue Count: 198 
• Unique protein chains: 1

1BDQ

HIV-1 (2:31-37, 47, 82) PROTEASE COMPLEXED WITH INHIBITOR SB203386

• DOI: 10.2210/pdb1BDQ/pdb

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


• Deposited: 1998-05-10 Released: 1998-08-12 
• Deposition Author(s): Swairjo, M.A., Abdel-Meguid, S.S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.261 
• R-Value Work: 0.191 

Literature

Structural role of the 30's loop in determining the ligand specificity of the human immunodeficiency virus protease.

Swairjo, M.A., Towler, E.M., Debouck, C., Abdel-Meguid, S.S.

(1998) Biochemistry 37: 10928-10936

• PubMed: 9692985 
• DOI: 10.1021/bi980784h
• Primary Citation of Related Structures:  
  1BDR, 1BDL


• PubMed Abstract: 
  

The structural basis of ligand specificity in human immunodeficiency virus (HIV) protease has been investigated by determining the crystal structures of three chimeric HIV proteases complexed with SB203386, a tripeptide analogue inhibitor. The chimeras are constructed by substituting amino acid residues in the HIV type 1 (HIV-1) protease sequence with the corresponding residues from HIV type 2 (HIV-2) in the region spanning residues 31-37 and in the active site cavity. SB203386 is a potent inhibitor of HIV-1 protease (Ki = 18 nM) but has a decreased affinity for HIV-2 protease (Ki = 1280 nM). Crystallographic analysis reveals that substitution of residues 31-37 (30's loop) with those of HIV-2 protease renders the chimera similar to HIV-2 protease in both the inhibitor binding affinity and mode of binding (two inhibitor molecules per protease dimer). However, further substitution of active site residues 47 and 82 has a compensatory effect which restores the HIV-1-like inhibitor binding mode (one inhibitor molecule in the center of the protease active site) and partially restores the affinity. Comparison of the three chimeric protease structures with those of HIV-1 and SIV proteases complexed with the same inhibitor reveals structural changes in the flap regions and the 80's loops, as well as changes in the dimensions of the active site cavity. The study provides structural evidence of the role of the 30's loop in conferring inhibitor specificity in HIV proteases.

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Related Citations: 

• Identification of a Loop Outside the Active Site Cavity of the Human Immunodeficiency Virus Proteases which Confers Inhibitor Specificity
  Towler, E.M.,Thompson, S.K.,Tomaszek, T.,Debouck, C.
  (1997) Biochemistry 36: 5128




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Organizational Affiliation: 

Department of Structural Biology and Molecular Biology, SmithKline Beecham Pharmaceuticals, King of Prussia, Pennsylvania 19406, 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	Mutation(s): 9  Gene Names: gag-pol
Find proteins for P04587 (Human immunodeficiency virus type 1 group M subtype B) Go to UniProtKB:  P04587

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
IM1	B	(2R,4S,5S,1'S)-2-PHENYLMETHYL-4-HYDROXY-5-(TERT-BUTOXYCARBONYL)AMINO-6-PHENYL HEXANOYL-N-(1'-IMIDAZO-2-YL)-2'-METHYLPROPANAMIDE C31 H42 N4 O4 QAHXABIFJPGWDD-WKAQUBQDSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
IM1	Ki: 460 nM BINDINGMOAD
IM1	Ki: 460 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.5 Å
• R-Value Free: 0.261 
• R-Value Work: 0.191 
• Space Group: P 6₁

Unit Cell:

Length (Å)	Angle (°)
a = 62.910	α = 90.00
b = 62.910	β = 90.00
c = 83.560	γ = 120.00

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1998-05-10 
• Released Date: 1998-08-12 
• Deposition Author(s): Swairjo, M.A., Abdel-Meguid, S.S.

Revision History 

• Version 1.0: 1998-08-12
  Type: Initial release
• Version 1.1: 2008-03-03
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance