Download MendeleyIn 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.
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
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.245
- R-Value Work: 0.216
This is version 1.6 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Gag-Pol polyprotein | 99 | Human immunodeficiency virus 1 | Mutation(s): 8 |  | |
UniProt | |||||
Find proteins for Q7SMT3 (Human immunodeficiency virus 1) Explore Q7SMT3 Go to UniProtKB: Q7SMT3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q7SMT3 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| RIT Query on RIT | D [auth B] | RITONAVIR C37 H48 N6 O5 S2 NCDNCNXCDXHOMX-XGKFQTDJSA-N |  | ||
| GOL Query on GOL | C [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| Binding Affinity Annotations | |||
|---|---|---|---|
| ID | Source | Binding Affinity | |
| RIT | BindingDB: 2B60 | Ki: min: 0.01, max: 109 (nM) from 27 assay(s) | |
| Kd: min: 0.6, max: 0.61 (nM) from 2 assay(s) | |||
| IC50: 67 (nM) from 1 assay(s) | |||
| -TΔS: min: -1.02e+2, max: -3.01e+1 (kJ/mol) from 29 assay(s) | |||
| ΔH: min: -2.76e+1, max: 73.15 (kJ/mol) from 28 assay(s) | |||
| ΔG: min: -6.02e+1, max: -2.88e+1 (kJ/mol) from 27 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 | | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.245
- R-Value Work: 0.216
- 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 Name | Purpose |
|---|---|
| DENZO | data reduction |
| SCALEPACK | data scaling |
| CNS | refinement |
| PDB_EXTRACT | data extraction |
| CNS | phasing |
Entry History
Deposition Data
- Released Date: 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.
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
