3NDX

HIV-1 Protease Saquinavir:Ritonavir 1:50 complex structure

• PDB DOI: https://doi.org/10.2210/pdb3NDX/pdb

• Classification: hydrolase/hydrolase inhibitor
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2010-06-08 Released: 2011-07-20 
• Deposition Author(s): Geremia, S., Olajuyigbe, F.M., Demitri, N.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.03 Å
• R-Value Free: 
  0.170 (DCC) 
• R-Value Work: 
  0.130 (DCC) 

Literature

Investigation of 2-Fold Disorder of Inhibitors and Relative Potency by Crystallizations of HIV-1 Protease in Ritonavir and Saquinavir Mixtures

Olajuyigbe, F.M., Demitri, N., Geremia, S.

(2011) Cryst Growth Des 11: 4378-4385

• DOI: https://doi.org/10.1021/cg200514z

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: 22.93 kDa 
• Atom Count: 2,053 
• 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	Human immunodeficiency virus 1	Mutation(s): 5  Gene Names: 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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
RIT	C [auth A]	RITONAVIR C37 H48 N6 O5 S2 NCDNCNXCDXHOMX-XGKFQTDJSA-N
SO4	G [auth B], L [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	E [auth A], H [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	D [auth A], I [auth B], J [auth B], K [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
CL	F [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Binding Affinity Annotations
ID	Source	Binding Affinity
RIT	BindingDB:  3NDX	Ki: min: 0.02, max: 0.23 (nM) from 2 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: 1.03 Å
• R-Value Free:  0.170 (DCC) 
• R-Value Work:  0.130 (DCC) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 51.16	α = 90
b = 58.567	β = 90
c = 61.143	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SHELX	model building
SHELXL-97	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-07-20 
Deposition Author(s): Geremia, S., Olajuyigbe, F.M., Demitri, N.

Revision History  

• Version 1.0: 2011-07-20
  Type: Initial release
  
• Version 1.1: 2011-12-07
  Changes: Database references
• Version 1.2: 2012-12-12
  Changes: Other
• Version 1.3: 2024-02-21
  Changes: Data collection, Database references, Derived calculations