4RVX | pdb_00004rvx

Crystal structure of multidrug-resistant clinical isolate A02 HIV-1 protease in complex with non-peptidic inhibitor, GRL079

PDB DOI: https://doi.org/10.2210/pdb4RVX/pdb

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

Deposited: 2014-11-28 Released: 2016-05-04
Deposition Author(s): Yedidi, R.S., Garimella, H., Kaufman, J.D., Das, D., Wingfield, P.T., Ghosh, A.K., Mitsuya, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free:
0.232 (Depositor), 0.232 (DCC)
R-Value Work:
0.190 (Depositor), 0.192 (DCC)
R-Value Observed:
0.192 (Depositor)

wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Enhanced antiviral activity by the P2-tris-tetrahydrofuran moiety of GRL-0519, a novel nonpeptidic HIV-1 protease inhibitor (PI), against multi-PI-resistant and highly darunavir-resistant strains of HIV-1.

Yedidi, R.S., Maeda, K., Aoki, M., Garimella, H., Rao, K.V., Akasapu, S., Davis, D.A., Kaufman, J.D., Das, D., Wingfield, P.T., Amano, M., Ghosh, A.K., Mitsuya, H.

To be published.

Macromolecule Content

Total Structure Weight: 44.62 kDa
Atom Count: 3,356
Modeled Residue Count: 396
Deposited Residue Count: 396
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
HIV-1 Protease	A, B, C, D	99	Human immunodeficiency virus 1	Mutation(s): 1 Gene Names: pol
UniProt
Find proteins for Q9J006 (Human immunodeficiency virus type 1) Explore Q9J006 Go to UniProtKB: Q9J006
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9J006
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
79G Query on 79G Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth D] MOL2 format, chain E [auth A] MOL2 format, chain F [auth D] mmCIF format, chain E [auth A] mmCIF format, chain F [auth D]	E [auth A], F [auth D]	(4S)-4-amino-N-[(2S,3S)-3-hydroxy-4-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}-1-phenylbutan-2-yl]-3,4-dihydro-2H-chromene-6-carboxamide C₃₁ H₃₉ N₃ O₆ S YPJHJNRFPZWLPW-AWCRTANDSA-N		Interactions Focus chain E [auth A] Focus chain F [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.96 Å
R-Value Free: 0.232 (Depositor), 0.232 (DCC)
R-Value Work: 0.190 (Depositor), 0.192 (DCC)
R-Value Observed: 0.192 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 53.789	α = 90
b = 89.008	β = 112.98
c = 56.513	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-05-04

Deposition Author(s):

Wingfield, P.T.

Revision History (Full details and data files)

Version 1.0: 2016-05-04
Type: Initial release
Version 1.1: 2024-02-28
Changes: Data collection, Database references, Derived calculations

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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.