6OGR | pdb_00006ogr

X-ray crystal structure of darunavir-resistant HIV-1 protease (P30) in complex with GRL-142

PDB DOI: https://doi.org/10.2210/pdb6OGR/pdb

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

Deposited: 2019-04-03 Released: 2020-04-08
Deposition Author(s): Bulut, H., Hattori, S.I., Aoki-Ogata, H., Hayashi, H., Aoki, M., Ghosh, A.K., Mitsuya, H.
Funding Organization(s): National Institutes of Health/National Cancer Institute (NIH/NCI)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.28 Å
R-Value Free:
0.229 (Depositor), 0.241 (DCC)
R-Value Work:
0.207 (Depositor), 0.215 (DCC)
R-Value Observed:
0.208 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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Literature

Novel HIV-1 protease inhibitors, GRL-142 and its analogs, markedly adapt to the structural plasticity of HIV-1 protease and exerts extreme potency with high genetic barrier

Bulut, H., Hattori, S.I., Aoki-Ogata, H., Hayashi, H., Aoki, M., Ghosh, A.K., Mitsuya, H.

To be published.

Macromolecule Content

Total Structure Weight: 11.55 kDa
Atom Count: 880
Modeled Residue Count: 99
Deposited Residue Count: 99
Unique protein chains: 1

Macromolecules

Find similar proteins by:

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 O38885 (Human immunodeficiency virus type 1) Explore O38885 Go to UniProtKB: O38885
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O38885
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7OA (Subject of Investigation/LOI) Query on 7OA 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]	(3S,3aR,5R,7aS,8S)-hexahydro-4H-3,5-methanofuro[2,3-b]pyran-8-yl [(2S,3R)-4-[{[2-(cyclopropylamino)-1,3-benzothiazol-6-yl]sulfonyl}(2-methylpropyl)amino]-1-(3,5-difluorophenyl)-3-hydroxybutan-2-yl]carbamate C₃₃ H₄₀ F₂ N₄ O₇ S₂ ARWGTMGGJGADTI-VFGYXJDYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
EDO Query on EDO 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]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-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: 1.28 Å
R-Value Free: 0.229 (Depositor), 0.241 (DCC)
R-Value Work: 0.207 (Depositor), 0.215 (DCC)
R-Value Observed: 0.208 (Depositor)

Space Group: P 6₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.845	α = 90
b = 62.845	β = 90
c = 81.808	γ = 120

Software Package:

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

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-04-08

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: 2020-04-08
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description

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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.