3NLS | pdb_00003nls

Crystal Structure of HIV-1 Protease in Complex with KNI-10772

• PDB DOI: https://doi.org/10.2210/pdb3NLS/pdb

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


• Deposited: 2010-06-21 Released: 2011-09-07 
• Deposition Author(s): Gabelli, S.B., Kawasaki, Y., Freire, E., Amzel, L.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free: 
  0.218 (Depositor), 0.218 (DCC) 
• R-Value Work: 
  0.179 (Depositor), 0.179 (DCC) 
• R-Value Observed: 
  0.181 (Depositor) 

Literature

Crystal Structure of HIV-1 Protease in Complex with KNI-10772

Kawasaki, Y., Gabelli, S.B., Amzel, L.M., Freire, E.

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: 22.47 kDa 
• Atom Count: 1,933 
• Modeled 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 type 1 (BRU ISOLATE)	Mutation(s): 3  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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
016	E [auth B]	(4R)-3-[(2R,3S)-3-{[(2,6-dimethylphenoxy)acetyl]amino}-2-hydroxy-4-phenylbutanoyl]-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H- inden-1-yl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide C35 H41 N3 O6 S KKTYZYHUPKXLPL-IUHSWKRHSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
DMS	F [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
URE	D [auth A]	UREA C H4 N2 O XSQUKJJJFZCRTK-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 4
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000572 (016)	E [auth B]	KNI-10772	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.70 Å
• R-Value Free:  0.218 (Depositor), 0.218 (DCC) 
• R-Value Work:  0.179 (Depositor), 0.179 (DCC) 
• R-Value Observed: 0.181 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.896	α = 90
b = 85.389	β = 90
c = 46.691	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-09-07 
Deposition Author(s): Gabelli, S.B., Kawasaki, Y., Freire, E., Amzel, L.M.

Revision History  

• Version 1.0: 2011-09-07
  Type: Initial release
  
• Version 1.1: 2012-12-12
  Changes: Other
• Version 1.2: 2024-02-21
  Changes: Data collection, Database references, Derived calculations, Structure summary