2QAK

HIV-1 PR mutant in complex with nelfinavir

PDB DOI: https://doi.org/10.2210/pdb2QAK/pdb

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

Deposited: 2007-06-16 Released: 2008-07-01
Deposition Author(s): Rezacova, P., Kozisek, M., Saskova, K., Brynda, J., Konvalinka, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.236
R-Value Work: 0.203
R-Value Observed: 0.205

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Evolutionary pathway of HIV resistance analyzed on molecular level: Enzymatic activities, 3-D structures and thermodynamics of HIV proteases resistant to nelfinavir

Kozisek, M., Bray, J., Rezacova, P., Saskova, K., Rulisek, L., Brynda, J., Pokorna, J., Mammano, F., Konvalinka, J.

To be published.

Macromolecule Content

Total Structure Weight: 22.09 kDa
Atom Count: 1,696
Modelled Residue Count: 198
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PROTEASE RETROPEPSIN	A, B	99	Human immunodeficiency virus 1	Mutation(s): 3 Gene Names: gag-pol EC: 3.4.23.16
UniProt
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)) Explore P03367 Go to UniProtKB: P03367
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P03367
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
1UN Query on 1UN Download Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A]	C [auth A]	2-[2-HYDROXY-3-(3-HYDROXY-2-METHYL-BENZOYLAMINO)-4-PHENYL SULFANYL-BUTYL]-DECAHYDRO-ISOQUINOLINE-3-CARBOXYLIC ACID TERT-BUTYLAMIDE C₃₂ H₄₅ N₃ O₄ S QAGYKUNXZHXKMR-HKWSIXNMSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
1UN	BindingDB: 2QAK	Ki: min: 0.07, max: 2 (nM) from 2 assay(s)
		Kd: min: 3, max: 38 (nM) from 3 assay(s)
		IC50: min: 1.9, max: 530 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.236
R-Value Work: 0.203
R-Value Observed: 0.205
Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.5	α = 90
b = 62.5	β = 90
c = 82.06	γ = 120

Software Package:

Software Name	Purpose
MAR345dtb	data collection
MOLREP	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2008-07-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2008-07-01
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2021-10-20
Changes: Database references, Derived calculations
Version 1.3: 2023-08-30
Changes: Data collection, Refinement description

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.