1RL8 | pdb_00001rl8

Crystal structure of the complex of resistant strain of hiv-1 protease(v82a mutant) with ritonavir

• PDB DOI: https://doi.org/10.2210/pdb1RL8/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2003-11-25 Released: 2005-04-19 
• Deposition Author(s): Rezacova, P., Brynda, J., Sedlacek, J., Konvalinka, J., Fabry, M., Horejsi, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.269 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.226 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the complex of resistant strain of hiv-1 protease(v82a mutant) with ritonavir

Rezacova, P., Brynda, J., Sedlacek, J., Konvalinka, J., Fabry, M., Horejsi, M.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

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

Macromolecule Content 

• Total Structure Weight: 22.1 kDa 
• Atom Count: 1,743 
• Modeled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protease RETROPEPSIN	A, B	99	Human immunodeficiency virus 1	Mutation(s): 2  Gene Names: gag-pol EC: 3.4.23.16
UniProt
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)) Explore P03367  Go to UniProtKB:  P03367

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RIT	C [auth A]	RITONAVIR C37 H48 N6 O5 S2 NCDNCNXCDXHOMX-XGKFQTDJSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
RIT	BindingDB:  1RL8	Ki: min: 1.1, max: 932 (nM) from 9 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001001 (RIT)	C [auth A]	RITONAVIR	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.269 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.226 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.414	α = 90
b = 61.414	β = 90
c = 80.816	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
SHELX	refinement
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-04-19 
Deposition Author(s): Rezacova, P., Brynda, J., Sedlacek, J., Konvalinka, J., Fabry, M., Horejsi, M.

Revision History  

• Version 1.0: 2005-04-19
  Type: Initial release
  
• Version 1.1: 2008-04-29
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2013-02-27
  Changes: Other
• Version 1.4: 2021-10-27
  Changes: Data collection, Database references, Derived calculations
• Version 1.5: 2023-08-23
  Changes: Data collection, Refinement description