2F3K

Substrate envelope and drug resistance: crystal structure of r01 in complex with wild-type hiv-1 protease


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 

wwPDB Validation   3D Report Full Report


This is version 1.3 of the entry. See complete history


Literature

Substrate envelope and drug resistance: crystal structure of RO1 in complex with wild-type human immunodeficiency virus type 1 protease.

Prabu-Jeyabalan, M.King, N.M.Nalivaika, E.A.Heilek-Snyder, G.Cammack, N.Schiffer, C.A.

(2006) Antimicrob Agents Chemother 50: 1518-1521

  • DOI: 10.1128/AAC.50.4.1518-1521.2006
  • Primary Citation of Related Structures:  
    2F3K

  • PubMed Abstract: 
  • In our previous crystallographic studies of human immunodeficiency virus type 1 (HIV-1) protease-substrate complexes, we described a conserved "envelope" that appears to be important for substrate recognition and the selection of drug-resistant mutat ...

    In our previous crystallographic studies of human immunodeficiency virus type 1 (HIV-1) protease-substrate complexes, we described a conserved "envelope" that appears to be important for substrate recognition and the selection of drug-resistant mutations. In this study, the complex of HIV-1 protease with the inhibitor RO1 was determined and comparison with the substrate envelope provides a rationale for mutational patterns.


    Organizational Affiliation

    Department of Biochemistry & Molecular Pharmacology, University of Massachusetts Medical School, 364 Plantation St., Worcester, MA 01605, USA.



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
ProteaseAB99Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: pol
EC: 3.4.23.16
Find proteins for O38708 (Human immunodeficiency virus 1)
Explore O38708 
Go to UniProtKB:  O38708
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
RO1
Query on RO1

Download CCD File 
A
(3S,4AS,8AS)-N-(TERT-BUTYL)-2-[(3S)-3-({3-(METHYLSULFONYL)-N-[(PYRIDIN-3-YLOXY)ACETYL]-L-VALYL}AMINO)-2-OXO-4-PHENYLBUTYL]DECAHYDROISOQUINOLINE-3-CARBOXAMIDE
C37 H53 N5 O7 S
NHCWVIKQVTUOGE-HAMVXVSQSA-N
 Ligand Interaction
PO4
Query on PO4

Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RO1IC50 :  13   nM  PDBBind
RO1Kd:  0.949999988079071   nM  Binding MOAD
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.60 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.163 
  • R-Value Observed: 0.165 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 50.873α = 90
b = 58.167β = 90
c = 61.653γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2006-11-21
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description