2B7Z

Structure of HIV-1 protease mutant bound to indinavir

• PDB DOI: https://doi.org/10.2210/pdb2B7Z/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2005-10-05 Released: 2006-11-14 
• Deposition Author(s): Clemente, J.C., Stow, L.R., Janka, L.K., Jeung, J.A., Desai, K.A., Govindasamy, L., Agbandje-McKenna, M., McKenna, R., Goodenow, M.M., Dunn, B.M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.254 
• R-Value Work: 0.216 
• R-Value Observed: 0.209 

Literature

In vivo, kinetic, and structural analysis of the development of ritonavir resistance

Clemente, J.C., Stow, L.R., Janka, L.K., Jeung, J.A., Desai, K.A., Govindasamy, L., Agbandje-McKenna, M., McKenna, R., Goodenow, M.M., Dunn, B.M.

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,PQS (software)

Macromolecule Content

• Total Structure Weight: 22.28 kDa 
• Atom Count: 1,705 
• Modelled Residue Count: 198 
• Deposited Residue Count: 198 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 protease	A [auth B], B [auth A]	99	Human immunodeficiency virus 1	Mutation(s): 10
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 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MK1	C [auth B]	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

Binding Affinity Annotations
ID	Source	Binding Affinity
MK1	BindingDB:  2B7Z	Ki: min: 62, max: 4235 (nM) from 7 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 0.254 
• R-Value Work: 0.216 
• R-Value Observed: 0.209 
• Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.831	α = 90
b = 61.831	β = 90
c = 84.033	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-11-14 
Deposition Author(s): Clemente, J.C., Stow, L.R., Janka, L.K., Jeung, J.A., Desai, K.A., Govindasamy, L., Agbandje-McKenna, M., McKenna, R., Goodenow, M.M., Dunn, B.M.

Revision History  

• Version 1.0: 2006-11-14
  Type: Initial release
  
• Version 1.1: 2008-04-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Derived calculations, Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2021-10-20
  Changes: Database references, Derived calculations
• Version 1.5: 2024-02-14
  Changes: Data collection