9CTX | pdb_00009ctx

X-ray crystal structure of multi-drug resistant HIV-1 protease (P51) in complex with Darunavir

• PDB DOI: https://doi.org/10.2210/pdb9CTX/pdb

• Classification: VIRAL PROTEIN
• Organism(s): Human immunodeficiency virus 1
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2024-07-25 Released: 2024-08-07 
• Deposition Author(s): Hayashi, H., Yedidi, R., Bulut, H., Das, D., Mitsuya, H.
• Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.165 (Depositor), 0.180 (DCC) 
• R-Value Observed: 
  0.167 (Depositor) 

Starting Model: experimental

Literature

Secondary amino-acid substitutions contribute to the emergence of HIV protease inhibitor resistance as directly as primary amino-acid substitutions.

Das, D., Hayashi, H., Yedidi, R.S., Bulut, H., Mitsuya, H.

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)

Biological Assembly Evidence: gel filtration

Macromolecule Content 

• Total Structure Weight: 11.52 kDa 
• Atom Count: 893 
• Modeled Residue Count: 99 
• Deposited Residue Count: 99 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Protease	A	99	Human immunodeficiency virus 1	Mutation(s): 0  Gene Names: pol
UniProt
Find proteins for O38893 (Human immunodeficiency virus type 1) Explore O38893  Go to UniProtKB:  O38893

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
017 (Subject of Investigation/LOI)	B [auth A]	(3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE C27 H37 N3 O7 S CJBJHOAVZSMMDJ-HEXNFIEUSA-N
GOL	C [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.208 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.165 (Depositor), 0.180 (DCC) 
• R-Value Observed: 0.167 (Depositor) 

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.68	α = 90
b = 62.68	β = 90
c = 81.759	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
xia2	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2024-08-07 
Deposition Author(s): Hayashi, H., Yedidi, R., Bulut, H., Das, D., Mitsuya, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Cancer Institute (NIH/NCI)	United States	--

Revision History  

• Version 1.0: 2024-08-07
  Type: Initial release