3SAC | pdb_00003sac

Crystal structure of wild-type HIV-1 protease in complex with AF80

• PDB DOI: https://doi.org/10.2210/pdb3SAC/pdb

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


• Deposited: 2011-06-02 Released: 2012-06-06 
• Deposition Author(s): Schiffer, C.A., Nalam, M.N.L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.204 (Depositor), 0.213 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.191 (DCC) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Protease Inhibitors that protrude out from substrate envelope are more susceptible to developing drug resistance

Altman, M.D., Nalam, M.N.L., Ali, A., Cao, H., Rana, T.M., Schiffer, C.A., Tidor, B.

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: 22.39 kDa 
• Atom Count: 1,748 
• 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 1	Mutation(s): 1  Gene Names: gag-pol, pol
UniProt
Find proteins for O38732 (Human immunodeficiency virus type 1) Explore O38732  Go to UniProtKB:  O38732

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
AF8	E [auth B]	3-hydroxy-N-{(2S,3R)-3-hydroxy-4-[(2-methylpropyl){[5-(1,2-oxazol-5-yl)thiophen-2-yl]sulfonyl}amino]-1-phenylbutan-2-yl}benzamide C28 H31 N3 O6 S2 YMMHVVLAGFSMTG-BJKOFHAPSA-N
PO4	C [auth A], D [auth A]	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000955 (AF8)	E [auth B]	3-HYDROXY-N-{(2S,3R)-3-HYDROXY-4-[(2-METHYLPROPYL){[5-(1,2-OXAZOL-5-YL)THIOPHEN-2-YL]SULFONYL}AMINO]-1-PHENYLBUTAN-2-YL}BENZAMIDE	Peptide-like / Inhibitor

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.204 (Depositor), 0.213 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.191 (DCC) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.88	α = 90
b = 58.001	β = 90
c = 61.567	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
HKL-2000	data reduction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-06-06 
Deposition Author(s): Schiffer, C.A., Nalam, M.N.L.

Revision History  

• Version 1.0: 2012-06-06
  Type: Initial release
  
• Version 1.1: 2012-12-12
  Changes: Other
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-09-13
  Changes: Data collection, Database references, Derived calculations, Refinement description