Macromolecule Content

Total Structure Weight: 22.10 kDa
Atom Count: 1743
Residue Count: 198
Unique protein chains: 1

1RL8

Crystal structure of the complex of resistant strain of hiv-1 protease(v82a mutant) with ritonavir

DOI: 10.2210/pdb1RL8/pdb

Classification: HYDROLASE/HYDROLASE INHIBITOR
Organism(s): Human immunodeficiency virus 1
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2003-11-25 Released: 2005-04-19
Deposition Author(s): Rezacova, P., Brynda, J., Sedlacek, J., Konvalinka, J., Fabry, M., Horejsi, M.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.269
R-Value Work: 0.226
R-Value Observed: 0.226

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the complex of resistant strain of hiv-1 protease(v82a mutant) with ritonavir

Rezacova, P., Brynda, J., Sedlacek, J., Konvalinka, J., Fabry, M., Horejsi, M.

To be published.

Macromolecules

Find similar proteins by:

(by identity cutoff) | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
protease RETROPEPSIN	A, B	99	Human immunodeficiency virus 1	Mutation(s): 2 Gene Names: gag-pol EC: 3.4.23.16 (PDB Primary Data), 2.7.7.49 (UniProt), 2.7.7.7 (UniProt), 3.1.26.13 (UniProt), 3.1.13.2 (UniProt), 2.7.7 (UniProt), 3.1 (UniProt)
Find proteins for P03367 (Human immunodeficiency virus type 1 group M subtype B (isolate BRU/LAI)) Explore P03367 Go to UniProtKB: P03367
Protein Feature View Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
RIT Query on RIT Download CCD File	A	RITONAVIR C₃₇ H₄₈ N₆ O₅ S₂ NCDNCNXCDXHOMX-XGKFQTDJSA-N		Ligand Interaction

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
RIT	-TΔS: 50.27000045776367 kJ/mol BindingDB
RIT	Ki: 15 nM BindingDB
RIT	ΔG: 42.63999938964844 kJ/mol BindingDB
RIT	ΔH: 51 kJ/mol BindingDB
RIT	-TΔS: 36.369998931884766 kJ/mol BindingDB
RIT	Ki: 98 nM BindingDB
RIT	ΔG: 44.310001373291016 kJ/mol BindingDB
RIT	ΔG: 49.31999969482422 kJ/mol BindingDB
RIT	ΔG: 60.189998626708984 kJ/mol BindingDB
RIT	ΔH: 17.559999465942383 kJ/mol BindingDB
RIT	Ki: 0.800000011920929 nM BindingDB
RIT	ΔH: 14.630000114440918 kJ/mol BindingDB
RIT	ΔG: 54.7599983215332 kJ/mol BindingDB
RIT	Ki: 23 nM BindingDB
RIT	-TΔS: 62.7599983215332 kJ/mol BindingDB
RIT	ΔG: 45.97999954223633 kJ/mol BindingDB
RIT	ΔG: 40.130001068115234 kJ/mol BindingDB
RIT	-TΔS: 51.0099983215332 kJ/mol BindingDB
RIT	ΔG: 55.18000030517578 kJ/mol BindingDB
RIT	-TΔS: 66.48999786376953 kJ/mol BindingDB
RIT	ΔH: 12.119999885559082 kJ/mol BindingDB
RIT	ΔH: 25.079999923706055 kJ/mol BindingDB
RIT	Ki: 0.3700000047683716 nM BindingDB
RIT	Ki: 60 nM BindingDB
RIT	ΔG: 44.72999954223633 kJ/mol BindingDB
RIT	ΔH: 15.050000190734863 kJ/mol BindingDB
RIT	-TΔS: 64.81999969482422 kJ/mol BindingDB
RIT	-TΔS: 44.75 kJ/mol BindingDB
RIT	Ki: 40 nM BindingDB
RIT	ΔH: 15.470000267028809 kJ/mol BindingDB
RIT	ΔG: 51.83000183105469 kJ/mol BindingDB
RIT	Ki: 0.05999999865889549 nM BindingDB
RIT	ΔG: 41.79999923706055 kJ/mol BindingDB
RIT	-TΔS: 33.040000915527344 kJ/mol BindingDB
RIT	ΔG: 35.529998779296875 kJ/mol BindingDB
RIT	ΔH: 26.75 kJ/mol BindingDB
RIT	-TΔS: 34.70000076293945 kJ/mol BindingDB
RIT	ΔH: 12.960000038146973 kJ/mol BindingDB
RIT	ΔG: 51.83000183105469 kJ/mol BindingDB
RIT	ΔH: 5.019999980926514 kJ/mol BindingDB
RIT	ΔH: 12.119999885559082 kJ/mol BindingDB
RIT	ΔG: 56.0099983215332 kJ/mol BindingDB
RIT	-TΔS: 60.63999938964844 kJ/mol BindingDB
RIT	ΔH: 15.470000267028809 kJ/mol BindingDB
RIT	-TΔS: 42.25 kJ/mol BindingDB
RIT	Kd: 0.6000000238418579 nM BindingDB
RIT	ΔG: 36.369998931884766 kJ/mol BindingDB
RIT	-TΔS: 58.59000015258789 kJ/mol BindingDB
RIT	ΔH: 40.130001068115234 kJ/mol BindingDB
RIT	-TΔS: 64.81999969482422 kJ/mol BindingDB
RIT	ΔG: 49.31999969482422 kJ/mol BindingDB
RIT	-TΔS: 76.94999694824219 kJ/mol BindingDB
RIT	ΔH: 40.130001068115234 kJ/mol BindingDB
RIT	ΔG: 45.13999938964844 kJ/mol BindingDB
RIT	ΔH: 22.56999969482422 kJ/mol BindingDB
RIT	-TΔS: 75.27999877929688 kJ/mol BindingDB
RIT	ΔG: 40.959999084472656 kJ/mol BindingDB
RIT	ΔG: 39.709999084472656 kJ/mol BindingDB
RIT	Ki: 30 nM BindingDB
RIT	Ki: 1.100000023841858 nM BindingDB
RIT	-TΔS: 42.63999938964844 kJ/mol BindingDB
RIT	Ki: 1.2000000476837158 nM BindingDB
RIT	ΔG: 53.5 kJ/mol BindingDB
RIT	ΔG: 53.5 kJ/mol BindingDB
RIT	-TΔS: 46.41999816894531 kJ/mol BindingDB
RIT	ΔG: 57.68000030517578 kJ/mol BindingDB
RIT	ΔG: 43.470001220703125 kJ/mol BindingDB
RIT	-TΔS: 43.91999816894531 kJ/mol BindingDB
RIT	ΔG: 56.43000030517578 kJ/mol BindingDB
RIT	-TΔS: 80.29000091552734 kJ/mol BindingDB
RIT	-TΔS: 79.04000091552734 kJ/mol BindingDB
RIT	-TΔS: 43.91999816894531 kJ/mol BindingDB
RIT	ΔG: 31.770000457763672 kJ/mol BindingDB
RIT	ΔH: 73.1500015258789 kJ/mol BindingDB
RIT	-TΔS: 58.560001373291016 kJ/mol BindingDB
RIT	Ki: 0.019999999552965164 nM BindingDB
RIT	-TΔS: 76.94999694824219 kJ/mol BindingDB
RIT	Ki: 109 nM BindingDB
RIT	IC50: 67 nM BindingDB
RIT	ΔH: 0 kJ/mol BindingDB
RIT	Ki: 32 nM BindingDB
RIT	ΔG: 52.25 kJ/mol BindingDB
RIT	ΔG: 28.84000015258789 kJ/mol BindingDB
RIT	ΔH: 27.59000015258789 kJ/mol BindingDB
RIT	-TΔS: 43.08000183105469 kJ/mol BindingDB
RIT	Ki: 0.20000000298023224 nM BindingDB
RIT	Ki: 0.23000000417232513 nM BindingDB
RIT	ΔH: 11.699999809265137 kJ/mol BindingDB
RIT	Ki: 3.0999999046325684 nM BindingDB
RIT	Ki: 2.809999942779541 nM BindingDB
RIT	-TΔS: 76.54000091552734 kJ/mol BindingDB
RIT	Ki: 0.9100000262260437 nM BindingDB
RIT	ΔG: 54.34000015258789 kJ/mol BindingDB
RIT	Ki: 0.46000000834465027 nM BindingDB
RIT	EC50: 150 nM BindingDB
RIT	ΔG: 50.15999984741211 kJ/mol BindingDB
RIT	Ki: 0.5899999737739563 nM BindingDB
RIT	ΔG: 38.040000915527344 kJ/mol BindingDB
RIT	Ki: 0.3700000047683716 nM BindingDB
RIT	IC50: 9850 nM BindingDB
RIT	ΔG: 33.439998626708984 kJ/mol BindingDB
RIT	ΔH: 21.739999771118164 kJ/mol BindingDB
RIT	ΔH: 13.789999961853027 kJ/mol BindingDB
RIT	Ki: 0.019999999552965164 nM BindingDB
RIT	ΔH: 43.470001220703125 kJ/mol BindingDB
RIT	Ki: 0.699999988079071 nM BindingDB
RIT	ΔH: 30.510000228881836 kJ/mol BindingDB
RIT	Ki: 13 nM BindingDB
RIT	ΔH: 35.95000076293945 kJ/mol BindingDB
RIT	ΔG: 38.869998931884766 kJ/mol BindingDB
RIT	-TΔS: 65.23999786376953 kJ/mol BindingDB
RIT	Ki: 2.4000000953674316 nM BindingDB
RIT	Kd: 0.6100000143051147 nM BindingDB
RIT	ΔG: 53.91999816894531 kJ/mol BindingDB
RIT	ΔH: 2.0899999141693115 kJ/mol BindingDB
RIT	-TΔS: 30.110000610351562 kJ/mol BindingDB
RIT	Ki: 0.699999988079071 nM BindingDB
RIT	-TΔS: 65.6500015258789 kJ/mol BindingDB
RIT	-TΔS: 45.59000015258789 kJ/mol BindingDB
RIT	ΔG: 52.66999816894531 kJ/mol BindingDB
RIT	ΔG: 36.779998779296875 kJ/mol BindingDB
RIT	ΔG: 34.279998779296875 kJ/mol BindingDB
RIT	-TΔS: 46.84000015258789 kJ/mol BindingDB
RIT	-TΔS: 102.05999755859375 kJ/mol BindingDB
RIT	ΔH: 12.960000038146973 kJ/mol BindingDB
RIT	ΔG: 45.560001373291016 kJ/mol BindingDB
RIT	Ki: 0.11999999731779099 nM BindingDB
RIT	-TΔS: 30.110000610351562 kJ/mol BindingDB
RIT	-TΔS: 57.33000183105469 kJ/mol BindingDB
RIT	ΔH: 4.599999904632568 kJ/mol BindingDB
RIT	ΔG: 49.7400016784668 kJ/mol BindingDB
RIT	ΔH: 12.539999961853027 kJ/mol BindingDB
RIT	-TΔS: 70.2699966430664 kJ/mol BindingDB
RIT	Ki: 0.5 nM BindingDB
RIT	-TΔS: 56.86000061035156 kJ/mol BindingDB
RIT	Ki: 0.05999999865889549 nM BindingDB
RIT	-TΔS: 57.29999923706055 kJ/mol BindingDB
RIT	Ki: 0.029999999329447746 nM BindingDB
RIT	ΔH: 9.609999656677246 kJ/mol BindingDB
RIT	ΔH: 12.119999885559082 kJ/mol BindingDB
RIT	ΔH: 2.930000066757202 kJ/mol BindingDB
RIT	ΔG: 45.560001373291016 kJ/mol BindingDB
RIT	ΔH: 12.960000038146973 kJ/mol BindingDB
RIT	-TΔS: 39.29999923706055 kJ/mol BindingDB
RIT	-TΔS: 69.83000183105469 kJ/mol BindingDB
RIT	-TΔS: 52.68000030517578 kJ/mol BindingDB
RIT	ΔG: 55.59000015258789 kJ/mol BindingDB
RIT	ΔH: 0.07999999821186066 kJ/mol BindingDB
RIT	Ki: 0.15000000596046448 nM BindingDB
RIT	ΔH: 17.969999313354492 kJ/mol BindingDB
RIT	Ki: 3.0199999809265137 nM BindingDB
RIT	Ki: 4.5 nM BindingDB
RIT	ΔH: 24.239999771118164 kJ/mol BindingDB
RIT	Ki: 4 nM BindingDB
RIT	ΔH: 10.869999885559082 kJ/mol BindingDB
RIT	-TΔS: 82.80000305175781 kJ/mol BindingDB
RIT	ΔH: 8.779999732971191 kJ/mol BindingDB
RIT	ΔH: 33.439998626708984 kJ/mol BindingDB
RIT	-TΔS: 35.540000915527344 kJ/mol BindingDB
RIT	ΔG: 57.27000045776367 kJ/mol BindingDB
RIT	ΔH: 3.759999990463257 kJ/mol BindingDB
RIT	-TΔS: 43.08000183105469 kJ/mol BindingDB
RIT	ΔH: 8.359999656677246 kJ/mol BindingDB
RIT	ΔG: 40.54999923706055 kJ/mol BindingDB
RIT	ΔH: 9.199999809265137 kJ/mol BindingDB
RIT	ΔH: 43.470001220703125 kJ/mol BindingDB

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_001001 (RIT) Query on PRD_001001	A	RITONAVIR	Peptide-like / Inhibitor		--

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.00 Å
R-Value Free: 0.269
R-Value Work: 0.226
R-Value Observed: 0.226
Space Group: P 6₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 61.414	α = 90
b = 61.414	β = 90
c = 80.816	γ = 120

Software Package:

Software Name	Purpose
CNS	refinement
SHELX	refinement
CNS	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2003-11-25
Released Date: 2005-04-19

Deposition Author(s):

Revision History

Version 1.0: 2005-04-19
Type: Initial release
Version 1.1: 2008-04-29
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

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Deposition Help & Resources

171588 Biological Macromolecular Structures Enabling Breakthroughs in Research and Education

1RL8

Crystal structure of the complex of resistant strain of hiv-1 protease(v82a mutant) with ritonavir

Crystal structure of the complex of resistant strain of hiv-1 protease(v82a mutant) with ritonavir

Entity ID: 1

Protein Feature View

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Entity ID: 2

Experimental Data

Structure Validation

Deposition Data

Revision History