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- PDB-3r0w: Crystal Structures of Multidrug-resistant HIV-1 Protease in Compl... -

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Basic information

Entry
Database: PDB / ID: 3r0w
TitleCrystal Structures of Multidrug-resistant HIV-1 Protease in Complex with Mechanism-Based Aspartyl Protease Inhibitors.
ComponentsMultidrug-resistant clinical isolate 769 HIV-1 Protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / host multivesicular body / RNA-directed DNA polymerase activity / endonuclease activity / aspartic-type endopeptidase activity / virion membrane / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
Reverse transcriptase thumb / Reverse transcriptase thumb domain / Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. ...Reverse transcriptase thumb / Reverse transcriptase thumb domain / Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
N-[(2R)-1-{[(2S,3S)-5-{[(2R)-1-{[(2S)-1-AMINO-4-METHYL-1-OXOPENTAN-2-YL]AMINO}-3-CHLORO-1-OXOPROPAN-2-YL]AMINO}-3-HYDROXY-5-OXO-1-PHENYLPENTAN-2-YL]AMINO}-3-METHYL-1-OXOBUTAN-2-YL]PYRIDINE-2-CARBOXAMIDE / Chem-RSY / Pol protein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsYedidi, R.S. / Gupta, D. / Liu, Z. / Brunzelle, J. / Kovari, I.A. / Woster, P.M. / Kovari, L.C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2012
Title: Crystal structures of multidrug-resistant HIV-1 protease in complex with two potent anti-malarial compounds.
Authors: Yedidi, R.S. / Liu, Z. / Wang, Y. / Brunzelle, J.S. / Kovari, I.A. / Woster, P.M. / Kovari, L.C. / Gupta, D.
History
DepositionMar 9, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 4, 2012Provider: repository / Type: Initial release
Revision 1.1Apr 25, 2012Group: Database references
Revision 1.2May 23, 2012Group: Database references
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Multidrug-resistant clinical isolate 769 HIV-1 Protease
B: Multidrug-resistant clinical isolate 769 HIV-1 Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1703
Polymers21,5392
Non-polymers6311
Water3,747208
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-20 kcal/mol
Surface area10650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.727, 45.727, 102.149
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein Multidrug-resistant clinical isolate 769 HIV-1 Protease


Mass: 10769.635 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q000H7
#2: Chemical ChemComp-RSY / N-[(2R)-1-{[(2S,3S)-5-{[(2R)-1-{[(2S)-1-amino-4-methyl-1-oxopentan-2-yl]amino}-3-chloro-1-oxopropan-2-yl]amino}-3-hydroxy-5-oxo-1-phenylpentan-2-yl]amino}-3-methyl-1-oxobutan-2-yl]pyridine-2-carboxamide


Type: peptide-like, Peptide-like / Class: Enzyme inhibitor / Mass: 631.163 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H43ClN6O6
References: N-[(2R)-1-{[(2S,3S)-5-{[(2R)-1-{[(2S)-1-AMINO-4-METHYL-1-OXOPENTAN-2-YL]AMINO}-3-CHLORO-1-OXOPROPAN-2-YL]AMINO}-3-HYDROXY-5-OXO-1-PHENYLPENTAN-2-YL]AMINO}-3-METHYL-1-OXOBUTAN-2-YL]PYRIDINE-2-CARBOXAMIDE
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.48 Å3/Da / Density % sol: 50.38 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.3 M NaCl, 0.1 M HEPES, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Sep 4, 2008
RadiationMonochromator: mirrors and beryllium lenses / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.7→50 Å / Num. obs: 22795 / Rmerge(I) obs: 0.04
Reflection shellResolution: 1.7→1.76 Å / % possible all: 100

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
HKL-2000data reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1TW7

1tw7


Resolution: 1.7→18.98 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.934 / SU B: 2.082 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R Free: 0.122 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1) DUE TO MULTIPLE BINDING ORIENTATIONS OF THE LIGAND, THE DIFFERENCE ELECTRON DENSITY (CALCULATED USING XTALVIEW/XFIT PROGRAM) WAS CONTOURED BETWEEN 1.8 AND 2.0 SIGMA WHILE FITTING THE ...Details: 1) DUE TO MULTIPLE BINDING ORIENTATIONS OF THE LIGAND, THE DIFFERENCE ELECTRON DENSITY (CALCULATED USING XTALVIEW/XFIT PROGRAM) WAS CONTOURED BETWEEN 1.8 AND 2.0 SIGMA WHILE FITTING THE LIGAND. EACH OF THE CONFORMATIONS WAS MANUALLY FIT INTO THE DENSITY AND REFINED USING REFMAC5. REFMAC LIBRARY FOR THE LIGAND WAS GENERATED USING MONOMER LIBRARY SKETCHER OPTION IN CCP4 AS WELL AS OBTAINED FROM PRODRG SERVER. REFINED COORDINATES FOR THE LIGAND CONFORMATION WITH HIGHEST OCCUPANCY AND REASONABLE THERMAL FACTOR VALUES ARE INCLUDED IN THE FINAL COORDINATE FILE. 2) HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.24539 1169 5.1 %RANDOM
Rwork0.19786 ---
obs0.20026 21607 99.46 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.058 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å20 Å20 Å2
2---0.02 Å20 Å2
3---0.05 Å2
Refinement stepCycle: LAST / Resolution: 1.7→18.98 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 44 208 1764
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221585
X-RAY DIFFRACTIONr_bond_other_d0.0010.029
X-RAY DIFFRACTIONr_angle_refined_deg1.52.0042154
X-RAY DIFFRACTIONr_angle_other_deg0.367318
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0225196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.7262556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.86615272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.731158
X-RAY DIFFRACTIONr_chiral_restr0.0980.2259
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021148
X-RAY DIFFRACTIONr_gen_planes_other0.0010.029
X-RAY DIFFRACTIONr_nbd_refined0.1970.2653
X-RAY DIFFRACTIONr_nbd_other0.1690.213
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21087
X-RAY DIFFRACTIONr_nbtor_other0.0990.22
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2114
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2440.265
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2510.21
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.220.231
X-RAY DIFFRACTIONr_mcbond_it1.1551.51005
X-RAY DIFFRACTIONr_mcangle_it1.7821596
X-RAY DIFFRACTIONr_scbond_it2.4593662
X-RAY DIFFRACTIONr_scangle_it3.9424.5558
LS refinement shellResolution: 1.7→1.746 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 77 -
Rwork0.221 1562 -
obs--99.88 %

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