6O48

Wild-type HIV-1 protease in complex with a substrate analog CA-p2


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.188 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Highly Drug-Resistant HIV-1 Protease Mutant PRS17 Shows Enhanced Binding to Substrate Analogues.

Agniswamy, J.Kneller, D.W.Brothers, R.Wang, Y.F.Harrison, R.W.Weber, I.T.

(2019) Acs Omega 4: 8707-8719

  • DOI: 10.1021/acsomega.9b00683
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • We report the structural analysis of highly drug-resistant human immunodeficiency virus protease (PR) variant PR <sup>S17 </sup>, rationally selected by machine learning, in complex with substrate analogues. Crystal structures were solved of inhibito ...

    We report the structural analysis of highly drug-resistant human immunodeficiency virus protease (PR) variant PR S17 , rationally selected by machine learning, in complex with substrate analogues. Crystal structures were solved of inhibitor-free inactive PR S17 -D25N, wild-type PR/CA-p2 complex, and PR S17 in complex with substrate analogues, CA-p2 and p2-NC. Peptide analogues p2-NC and CA-p2 exhibit inhibition constants of 514 and 22 nM, respectively, for PR S17 or approximately 3-fold better than for PR. CA-p2 is a better inhibitor of PR S17 than are clinical inhibitors ( K i = 50-8390 nM) except for amprenavir ( K i = 11 nM). G48V resistance mutation induces curled flap tips in PR S17 -D25N structure. The inner P2-P2' residues of substrate analogues in PR S17 complexes maintain similar conformations to those of wild-type complex, while significant conformational changes are observed in the peripheral residues P3, P4' of CA-p2 and P3, P4, and P3' of p2-NC. The loss of β-branched side chain by V82S mutation initiates a shift in 80's loop and reshapes the S3/S3' subsite, which enhances substrate binding with new hydrogen bonds and van der Waals interactions that are absent in the wild-type structures. The steric hindrance caused by G48V mutation in the flap of PR S17 contributes to altered binding interactions of P3 Arg, P4' norleucine of CA-p2, and P4 and P3' of p2-NC with the addition of new hydrogen bonds and van der Waals contacts. The enhanced interaction of PR S17 with substrate analogues agrees with their relative inhibition, suggesting that this mutant improves substrate binding while decreasing affinity for clinical inhibitors.


    Organizational Affiliation

    Department of Biology, Georgia State University, P.O. Box 4010, Atlanta, Georgia 30302, United States.,Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, Georgia 30302, United States.,Department of Computer Science, Georgia State University, P.O. Box 5060, Atlanta, Georgia 30302, United States.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
HIV-1 protease
A, B
99Human immunodeficiency virus type 1 group M subtype B (isolate BH10)Mutation(s): 5 
Gene Names: gag-pol
Find proteins for P03366 (Human immunodeficiency virus type 1 group M subtype B (isolate BH10))
Go to UniProtKB:  P03366
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
0Q4
Query on 0Q4

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B
N-[(2R)-2-({N~5~-[amino(iminio)methyl]-L-ornithyl-L-valyl}amino)-4-methylpentyl]-L-phenylalanyl-L-alpha-glutamyl-L-alanyl-L-norleucinamide
Inhibitor analogues of CA-p2
C40 H70 N11 O8
SGWAZUZKMXHYMB-UQGDEETHSA-O
 Ligand Interaction
NA
Query on NA

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A
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
FMT
Query on FMT

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A
FORMIC ACID
C H2 O2
BDAGIHXWWSANSR-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

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A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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B
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.46 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.188 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 58.407α = 90.00
b = 86.244β = 90.00
c = 46.581γ = 90.00
Software Package:
Software NamePurpose
SHELXLrefinement
AMoREphasing
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Human Genome Research Institute (NIH/NHGRI)United StatesGM062920

Revision History 

  • Version 1.0: 2019-06-19
    Type: Initial release
  • Version 1.1: 2019-07-17
    Type: Data collection, Structure summary
  • Version 1.2: 2019-08-28
    Type: Data collection, Refinement description
  • Version 1.3: 2019-12-18
    Type: Author supporting evidence