3EM4

Crystal structure of atazanavir (ATV) in complex with I50L/A71V drug-resistant HIV-1 protease

• PDB DOI: https://doi.org/10.2210/pdb3EM4/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): Prabu-Jeyabalan, M., King, N., Royer, C., Schiffer, C.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.249 
• R-Value Work: 0.179 
• R-Value Observed: 0.183 

Starting Model: experimental

Literature

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

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

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 45.39 kDa 
• Atom Count: 3,230 
• Modelled Residue Count: 396 
• Deposited Residue Count: 396 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B, C [auth U], D [auth V]	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
DR7	E [auth A], K [auth V]	(3S,8S,9S,12S)-3,12-BIS(1,1-DIMETHYLETHYL)-8-HYDROXY-4,11-DIOXO-9-(PHENYLMETHYL)-6-[[4-(2-PYRIDINYL)PHENYL]METHYL]-2,5, 6,10,13-PENTAAZATETRADECANEDIOIC ACID DIMETHYL ESTER C38 H52 N6 O7 AXRYRYVKAWYZBR-GASGPIRDSA-N
PO4	F [auth A], G [auth B], H [auth B], I [auth B], J [auth U], L [auth V], M [auth V]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Binding Affinity Annotations
ID	Source	Binding Affinity
DR7	BindingDB:  3EM4	Ki: min: 9.00e-3, max: 0.56 (nM) from 6 assay(s)
		Kd: 0.4 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.249 
• R-Value Work: 0.179 
• R-Value Observed: 0.183 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.231	α = 90
b = 59.54	β = 82.22
c = 59.863	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): Prabu-Jeyabalan, M., King, N., Royer, C., Schiffer, C.

Revision History  

• Version 1.0: 2009-09-01
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Advisory, Refinement description, Version format compliance
• Version 1.2: 2017-10-25
  Changes: Advisory, Refinement description
• Version 1.3: 2018-01-24
  Changes: Database references
• Version 1.4: 2021-10-20
  Changes: Advisory, Database references, Derived calculations, Structure summary
• Version 1.5: 2023-09-06
  Changes: Data collection, Refinement description
• Version 1.6: 2024-03-13
  Changes: Source and taxonomy, Structure summary