3EM6

Crystal structure of I50L/A71V mutant of hiv-1 protease in complex with inhibitor darunavir

• PDB DOI: https://doi.org/10.2210/pdb3EM6/pdb

• Classification: HYDROLASE
• Organism(s): HIV-1 M:B_ARV2/SF2
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2008-09-23 Released: 2009-09-01 
• Deposition Author(s): Royer, C.J., King, N.M., Prabu-Jeyabalan, M., Ng, C., Nalivaika, E.A., Schiffer, C.A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.240 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 

Starting Model: experimental

Literature

Kinetic and structural studies on atazanavir specific I50L drug-resistant HIV-1 protease mutant.

Prabu-Jeyabalan, M., Ng, C., King, N.M., Bandaranayake, R., Nalivaika, E.A., Schiffer, C.A.

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: 22.86 kDa 
• Atom Count: 1,673 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	99	HIV-1 M:B_ARV2/SF2	Mutation(s): 3  Gene Names: gag-pol, HIV-1 subtype B EC: 3.4.23.16
UniProt
Find proteins for P03369 (Human immunodeficiency virus type 1 group M subtype B (isolate ARV2/SF2)) Explore P03369  Go to UniProtKB:  P03369

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
017	C [auth A]	(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE C27 H37 N3 O7 S CJBJHOAVZSMMDJ-HEXNFIEUSA-N
PO4	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
ACT	G [auth A], J [auth B], K [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.240 
• R-Value Work: 0.186 
• R-Value Observed: 0.188 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.14	α = 90
b = 57.891	β = 90
c = 61.364	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-09-01 
Deposition Author(s): Royer, C.J., King, N.M., Prabu-Jeyabalan, M., Ng, C., Nalivaika, E.A., Schiffer, C.A.

Revision History  

• Version 1.0: 2009-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Refinement description
• Version 1.3: 2021-10-20
  Changes: Database references, Derived calculations, Structure summary
• Version 1.4: 2023-09-06
  Changes: Data collection, Refinement description
• Version 1.5: 2024-03-13
  Changes: Source and taxonomy, Structure summary