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.
2B7Z
Structure of HIV-1 protease mutant bound to indinavir
- PDB DOI: https://doi.org/10.2210/pdb2B7Z/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Human immunodeficiency virus 1
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2005-10-05 Released: 2006-11-14
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.254
- R-Value Work: 0.216
- R-Value Observed: 0.209
This is version 1.5 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 |
| HIV-1 protease | A [auth B], B [auth A] | 99 | Human immunodeficiency virus 1 | Mutation(s): 10 |  |
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 AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MK1 Query on MK1 | C [auth B] | N-[2(R)-HYDROXY-1(S)-INDANYL]-5-[(2(S)-TERTIARY
BUTYLAMINOCARBONYL)-4(3-PYRIDYLMETHYL)PIPERAZINO]-4(S)-HYDROXY-2(R)-PHENYLMETHYLPENTANAMIDE C36 H47 N5 O4 CBVCZFGXHXORBI-PXQQMZJSSA-N |  | ||
| Binding Affinity Annotations | |||
|---|---|---|---|
| ID | Source | Binding Affinity | |
| MK1 | BindingDB: 2B7Z | Ki: min: 0.05, max: 398 (nM) from 35 assay(s) | |
| Kd: 1.07 (nM) from 1 assay(s) | |||
| IC50: min: 0.36, max: 370 (nM) from 18 assay(s) | |||
| -TΔS: min: -7.40e+1, max: -2.80e+1 (kJ/mol) from 27 assay(s) | |||
| ΔH: min: -3.34e+1, max: 35.11 (kJ/mol) from 27 assay(s) | |||
| ΔG: min: -6.31e+1, max: -3.85e+1 (kJ/mol) from 28 assay(s) | |||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.20 Å
- R-Value Free: 0.254
- R-Value Work: 0.216
- R-Value Observed: 0.209
- Space Group: P 61
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 61.831 | α = 90 |
| b = 61.831 | β = 90 |
| c = 84.033 | 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: 2008-04-01
Changes: Version format compliance - Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance - Version 1.3: 2017-10-11
Changes: Refinement description - Version 1.4: 2021-10-20
Changes: Database references, Derived calculations - Version 1.5: 2024-02-14
Changes: Data collection
