3DOX | pdb_00003dox

X-ray structure of HIV-1 protease in situ product complex

• PDB DOI: https://doi.org/10.2210/pdb3DOX/pdb

• Classification: HYDROLASE
• Organism(s): HIV-1 M:B_HXB2R
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-07-07 Released: 2008-09-09 
• Deposition Author(s): Hosur, M.V., Ferrer, J.-L., Das, A., Prashar, V., Bihani, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.236 (Depositor), 0.237 (DCC) 
• R-Value Work: 
  0.197 (Depositor), 0.196 (DCC) 
• R-Value Observed: 
  0.197 (Depositor) 

Literature

X-ray structure of HIV-1 protease in situ product complex

Bihani, S., Das, A., Prashar, V., Ferrer, J.-L., Hosur, M.V.

(2009) Proteins 74: 594-602

• PubMed: 18704947 
• DOI: https://doi.org/10.1002/prot.22174
• Primary Citation Related Structures: 
  3DOX


• PubMed Abstract: 
  

  HIV-1 protease is an effective target for design of different types of drugs against AIDS. HIV-1 protease is also one of the few enzymes that can cleave substrates containing both proline and nonproline residues at the cleavage site. We report here the first structure of HIV-1 protease complexed with the product peptides SQNY and PIV derived by in situ cleavage of the oligopeptide substrate SQNYPIV, within the crystals. In the structure, refined against 2.0-A resolution synchrotron data, a carboxyl oxygen of SQNY is hydrogen-bonded with the N-terminal nitrogen atom of PIV. At the same time, this proline nitrogen atom does not form any hydrogen bond with catalytic aspartates. These two observations suggest that the protonation of scissile nitrogen, during peptide bond cleavage, is by a gem-hydroxyl of the tetrahedral intermediate rather than by a catalytic aspartic acid.

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Organizational Affiliation: 
• Solid State Physics Division, Bhabha Atomic Research Centre, Trombay, Mumbai 400085, India.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content 

• Total Structure Weight: 22.74 kDa 
• Atom Count: 1,766 
• Modeled Residue Count: 205 
• Deposited Residue Count: 210 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 PROTEASE	A	203	HIV-1 M:B_HXB2R	Mutation(s): 2  Gene Names: gag-pol EC: 3.4.23.16
UniProt
Find proteins for P04585 (Human immunodeficiency virus type 1 group M subtype B (isolate HXB2)) Explore P04585  Go to UniProtKB:  P04585

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
A PEPTIDE SUBSTRATE-SQNY	B [auth P]	4	N/A	Mutation(s): 0

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
A PEPTIDE SUBSTRATE-PIV	C [auth Q]	3	N/A	Mutation(s): 0

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.236 (Depositor), 0.237 (DCC) 
• R-Value Work:  0.197 (Depositor), 0.196 (DCC) 
• R-Value Observed: 0.197 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.38	α = 90
b = 62.38	β = 90
c = 82	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2008-09-09 
Deposition Author(s): Hosur, M.V., Ferrer, J.-L., Das, A., Prashar, V., Bihani, S.

Revision History  

• Version 1.0: 2008-09-09
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-09
  Changes: Advisory, Refinement description, Source and taxonomy
• Version 1.3: 2021-11-10
  Changes: Advisory, Database references
• Version 1.4: 2024-05-29
  Changes: Data collection