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: 1.599 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.163 

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

  • 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: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Protease
A, B
99Human immunodeficiency virus 1Mutation(s): 1 
Gene Names: pol
Find proteins for O38708 (Human immunodeficiency virus 1)
Go to UniProtKB:  O38708
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
PO4
Query on PO4

Download SDF File 
Download CCD File 
A, B
PHOSPHATE ION
O4 P
NBIIXXVUZAFLBC-UHFFFAOYSA-K
 Ligand Interaction
RO1
Query on RO1

Download SDF File 
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
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
RO1Kd: 0.95 nM BINDINGMOAD
RO1IC50: 13 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.599 Å
  • R-Value Free: 0.197 
  • R-Value Work: 0.163 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 50.873α = 90.00
b = 58.167β = 90.00
c = 61.653γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

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