3WSJ | pdb_00003wsj

HTLV-1 protease in complex with the HIV-1 protease inhibitor Indinavir

• PDB DOI: https://doi.org/10.2210/pdb3WSJ/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human T-cell leukemia virus type I
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-03-14 Released: 2014-10-22 
• Deposition Author(s): Kuhnert, M., Steuber, H., Diederich, W.E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.256 (Depositor), 0.259 (DCC) 
• R-Value Work: 
  0.205 (Depositor), 0.209 (DCC) 
• R-Value Observed: 
  0.209 (Depositor) 

Starting Model: experimental

Literature

Structural basis for HTLV-1 protease inhibition by the HIV-1 protease inhibitor indinavir.

Kuhnert, M., Steuber, H., Diederich, W.E.

(2014) J Med Chem 57: 6266-6272

• PubMed: 25006983 
• DOI: https://doi.org/10.1021/jm500402c
• Primary Citation Related Structures: 
  3WSJ


• PubMed Abstract: 
  

  HTLV-1 protease (HTLV-1 PR) is an aspartic protease which represents a promising drug target for the discovery of novel anti-HTLV-1 drugs. The X-ray structure of HTLV-1 PR in complex with the well-known and approved HIV-1 PR inhibitor Indinavir was determined at 2.40 Å resolution. In this contribution, we describe the first crystal structure in complex with a nonpeptidic inhibitor that accounts for rationalizing the rather moderate affinity of Indinavir against HTLV-1 PR and provides the basis for further structure-guided optimization strategies.

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Organizational Affiliation: 
• Institut für Pharmazeutische Chemie, Philipps-Universität Marburg , Marbacher Weg 6, 35032 Marburg, Germany.

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 - C3  (Explore in 3D)
Global Stoichiometry: Homo 6-mer - A6 

Biological assembly 2 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 27.19 kDa 
• Atom Count: 1,969 
• Modeled Residue Count: 232 
• Deposited Residue Count: 232 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	116	Human T-cell leukemia virus type I	Mutation(s): 1  Gene Names: prt
UniProt
Find proteins for Q82134 (Human T-cell leukemia virus type I) Explore Q82134  Go to UniProtKB:  Q82134

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MK1	C [auth A]	N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE C36 H47 N5 O4 CBVCZFGXHXORBI-PXQQMZJSSA-N
PG4	N [auth A]	TETRAETHYLENE GLYCOL C8 H18 O5 UWHCKJMYHZGTIT-UHFFFAOYSA-N
SO4	D [auth A], E [auth A], F [auth A], G [auth A], H [auth A], I [auth A], J [auth A], K [auth A], L [auth A], M [auth A], O [auth B], P [auth B], Q [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.256 (Depositor), 0.259 (DCC) 
• R-Value Work:  0.205 (Depositor), 0.209 (DCC) 
• R-Value Observed: 0.209 (Depositor) 

Space Group: P 6₃ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 77.26	α = 90
b = 77.26	β = 90
c = 159.34	γ = 120

Software Package:

Software Name	Purpose
MxCuBE	data collection
PHASER	phasing
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-10-22 
Deposition Author(s): Kuhnert, M., Steuber, H., Diederich, W.E.

Revision History  

• Version 1.0: 2014-10-22
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description