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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free:
0.208 (Depositor), 0.205 (DCC)
R-Value Work:
0.165 (Depositor), 0.164 (DCC)
R-Value Observed:
0.167 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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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.

Macromolecule Content

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

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O38893
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
017 (Subject of Investigation/LOI) Query on 017 Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	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		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
GOL Query on GOL Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.55 Å
R-Value Free: 0.208 (Depositor), 0.205 (DCC)
R-Value Work: 0.165 (Depositor), 0.164 (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

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Entry History

& Funding Information

Deposition Data

Released Date: 2024-08-07

Deposition Author(s):

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

Revision History (Full details and data files)

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

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.