6BRA | pdb_00006bra

HIV-1 protease (D25N, inactive) in complex with phage display optimized substrate SGIFLETS

• PDB DOI: https://doi.org/10.2210/pdb6BRA/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1, Enterobacteria phage fd
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2017-11-30 Released: 2018-07-18 
• Deposition Author(s): Windsor, I.W., Raines, R.T.
• Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.11 Å
• R-Value Free: 
  0.184 (Depositor), 0.185 (DCC) 
• R-Value Work: 
  0.171 (Depositor), 0.171 (DCC) 
• R-Value Observed: 
  0.171 (Depositor) 

Starting Model: experimental

Literature

A substrate selected by phage display exhibits enhanced side-chain hydrogen bonding to HIV-1 protease.

Windsor, I.W., Raines, R.T.

(2018) Acta Crystallogr D Struct Biol 74: 690-694

• PubMed: 29968678 
• DOI: https://doi.org/10.1107/S2059798318006691
• Primary Citation Related Structures: 
  6BRA


• PubMed Abstract: 
  

  Crystal structures of inactive variants of HIV-1 protease bound to peptides have revealed how the enzyme recognizes its endogenous substrates. The best of the known substrates is, however, a nonnatural substrate that was identified by directed evolution. The crystal structure of the complex between this substrate and the D25N variant of the protease is reported at a resolution of 1.1 Å. The structure has several unprecedented features, especially the formation of additional hydrogen bonds between the enzyme and the substrate. This work expands the understanding of molecular recognition by HIV-1 protease and informs the design of new substrates and inhibitors.

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Organizational Affiliation: 
• Department of Chemistry, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A2B1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local 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: 2,101 
• Modeled Residue Count: 206 
• Deposited Residue Count: 206 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A, B	99	Human immunodeficiency virus 1	Mutation(s): 6  Gene Names: pol
UniProt
Find proteins for Q5RZ08 (Human immunodeficiency virus type 1) Explore Q5RZ08  Go to UniProtKB:  Q5RZ08

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Phage display-optimized HIV-1 protease substrate	C [auth S]	8	Enterobacteria phage fd	Mutation(s): 0

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CL	D [auth A], E [auth A], F [auth A], G [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.11 Å
• R-Value Free:  0.184 (Depositor), 0.185 (DCC) 
• R-Value Work:  0.171 (Depositor), 0.171 (DCC) 
• R-Value Observed: 0.171 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.033	α = 90
b = 85.767	β = 90
c = 46.13	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data reduction
PHENIX	refinement
PDB_EXTRACT	data extraction
SCALEPACK	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-07-18 
Deposition Author(s): Windsor, I.W., Raines, R.T.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P41 GM103399
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM044783

Revision History  

• Version 1.0: 2018-07-18
  Type: Initial release
  
• Version 1.1: 2019-02-20
  Changes: Author supporting evidence, Data collection
• Version 1.2: 2020-01-01
  Changes: Author supporting evidence
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description