Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

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

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 21912.94 
• Atom Count: 1554 
• Residue Count: 198 
• Unique protein chains: 1

5KR1

Protease PR5-DRV

• DOI: 10.2210/pdb5KR1/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli K-12


• Deposited: 2016-07-06 Released: 2016-09-21 
• Deposition Author(s): Liu, Z., Poole, K.M., Mahon, B.P., McKenna, R., Fanucci, G.E.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences; National Institutes of Health/National Center for Research Resources; National Institutes of Health/National Institute Of Allergy and Infectious Diseases 

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.219 
• R-Value Work: 0.187 

Literature

Effects of Hinge-region Natural Polymorphisms on Human Immunodeficiency Virus-Type 1 Protease Structure, Dynamics, and Drug Pressure Evolution.

Liu, Z., Huang, X., Hu, L., Pham, L., Poole, K.M., Tang, Y., Mahon, B.P., Tang, W., Li, K., Goldfarb, N.E., Dunn, B.M., McKenna, R., Fanucci, G.E.

(2016) J.Biol.Chem. 291: 22741-22756

• PubMed: 27576689 
• DOI: 10.1074/jbc.M116.747568
• Primary Citation of Related Structures:  
  5KR2, 5KR0, 5KQZ, 5KQY, 5KQX


• PubMed Abstract: 
  

Multidrug resistance to current Food and Drug Administration-approved HIV-1 protease (PR) inhibitors drives the need to understand the fundamental mechanisms of how drug pressure-selected mutations, which are oftentimes natural polymorphisms, elicit their effect on enzyme function and resistance. Here, the impacts of the hinge-region natural polymorphism at residue 35, glutamate to aspartate (E35D), alone and in conjunction with residue 57, arginine to lysine (R57K), are characterized with the goal of understanding how altered salt bridge interactions between the hinge and flap regions are associated with changes in structure, motional dynamics, conformational sampling, kinetic parameters, and inhibitor affinity. The combined results reveal that the single E35D substitution leads to diminished salt bridge interactions between residues 35 and 57 and gives rise to the stabilization of open-like conformational states with overall increased backbone dynamics. In HIV-1 PR constructs where sites 35 and 57 are both mutated (e.g. E35D and R57K), x-ray structures reveal an altered network of interactions that replace the salt bridge thus stabilizing the structural integrity between the flap and hinge regions. Despite the altered conformational sampling and dynamics when the salt bridge is disrupted, enzyme kinetic parameters and inhibition constants are similar to those obtained for subtype B PR. Results demonstrate that these hinge-region natural polymorphisms, which may arise as drug pressure secondary mutations, alter protein dynamics and the conformational landscape, which are important thermodynamic parameters to consider for development of inhibitors that target for non-subtype B PR.

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Organizational Affiliation: 

From the Department of Chemistry, University of Florida, Gainesville, Florida 32611 and.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Protease PR5-DRV	A, B	99	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: pol
Find proteins for V5YAB1 (Human immunodeficiency virus 1) Go to UniProtKB:  V5YAB1

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
017	B	(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE Darunavir, TMC114, UIC-94017 C27 H37 N3 O7 S CJBJHOAVZSMMDJ-HEXNFIEUSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
017	Ki: 0 - 6.6 nM (86) BINDINGDB
017	Kd: 0 nM (86) BINDINGDB
017	EC50: 0.2 - 1.6 nM (89) BINDINGDB
017	IC50: 0.1 nM (86) BINDINGDB

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.6 Å
• R-Value Free: 0.219 
• R-Value Work: 0.187 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 50.960	α = 90.00
b = 58.000	β = 90.00
c = 61.730	γ = 90.00

Software Package:

Software Name	Purpose
PHASER	phasing
iMOSFLM	data reduction
PHENIX	refinement
Aimless	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Deposited Date: 2016-07-06 
• Released Date: 2016-09-21 
• Deposition Author(s): Liu, Z., Poole, K.M., Mahon, B.P., McKenna, R., Fanucci, G.E.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences	United States	GM105409
National Institutes of Health/National Center for Research Resources	United States	S10RR031603
National Institutes of Health/National Institute Of Allergy and Infectious Diseases	United States	R37 AI28571

Revision History 

• Version 1.0: 2016-09-21
  Type: Initial release
• Version 1.1: 2016-11-16
  Type: Database references
• Version 1.2: 2017-09-20
  Type: Author supporting evidence, Database references, Derived calculations