2B60

Structure of HIV-1 protease mutant bound to Ritonavir

PDB DOI: https://doi.org/10.2210/pdb2B60/pdb

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

Deposited: 2005-09-29 Released: 2006-11-14
Deposition Author(s): Clemente, J.C., Stow, L.R., Janka, L.K., Jeung, J.A., Desai, K.A., Govindasamy, L., Agbandje-McKenna, M., McKenna, R., Goodenow, M.M., Dunn, B.M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.245 (Depositor)
R-Value Work:
0.216 (Depositor), 0.210 (DCC)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.6 of the entry. See complete history.

Literature

In vivo, kinetic, and structural analysis of the development of ritonavir resistance

Clemente, J.C., Stow, L.R., Janka, L.K., Jeung, J.A., Desai, K.A., Govindasamy, L., Agbandje-McKenna, M., McKenna, R., Goodenow, M.M., Dunn, B.M.

To be published.

Macromolecule Content

Total Structure Weight: 22.54 kDa
Atom Count: 1,726
Modelled Residue Count: 198
Deposited Residue Count: 198
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gag-Pol polyprotein	A, B	99	Human immunodeficiency virus 1	Mutation(s): 8
UniProt
Find proteins for Q7SMT3 (Human immunodeficiency virus type 1) Explore Q7SMT3 Go to UniProtKB: Q7SMT3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q7SMT3
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RIT Query on RIT Download Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	RITONAVIR C₃₇ H₄₈ N₆ O₅ S₂ NCDNCNXCDXHOMX-XGKFQTDJSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
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]

Binding Affinity Annotations
ID	Source	Binding Affinity
RIT	BindingDB: 2B60	Ki: min: 30, max: 2107 (nM) from 9 assay(s)
		-TΔS: min: -2.72e+1, max: -5.84e+0 (kJ/mol) from 2 assay(s)
		ΔH: min: -2.63e+1, max: -9.61e+0 (kJ/mol) from 2 assay(s)
		ΔG: min: -3.68e+1, max: -3.22e+1 (kJ/mol) from 2 assay(s)

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001001 (RIT) Query on PRD_001001	D [auth B]	RITONAVIR	Peptide-like / Inhibitor		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.245 (Depositor)
R-Value Work: 0.216 (Depositor), 0.210 (DCC)

Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.979	α = 90
b = 61.979	β = 90
c = 84.247	γ = 120

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
CNS	refinement
PDB_EXTRACT	data extraction
CNS	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2006-11-14

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2006-11-14
Type: Initial release
Version 1.1: 2008-05-01
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
Version 1.3: 2013-02-27
Changes: Other
Version 1.4: 2017-10-11
Changes: Refinement description
Version 1.5: 2021-10-20
Changes: Database references, Derived calculations
Version 1.6: 2024-02-14
Changes: Data collection