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- PDB-4l1a: Crystallographic study of multi-drug resistant HIV-1 protease Lop... -

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Basic information

Entry
Database: PDB / ID: 4l1a
TitleCrystallographic study of multi-drug resistant HIV-1 protease Lopinavir complex: mechanism of drug recognition and resistance
Components(MDR769 HIV-1 protease) x 2
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV-1 protease / Multi-drug resistance / IC50 / Lopinavir / protease / 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 / RNA-directed DNA polymerase activity / endonuclease activity / aspartic-type endopeptidase activity / proteolysis / DNA binding
Similarity search - Function
Reverse transcriptase thumb / Reverse transcriptase thumb domain / Retropepsin-like catalytic domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic ...Reverse transcriptase thumb / Reverse transcriptase thumb domain / Retropepsin-like catalytic domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / 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
Chem-AB1 / Pol protein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsLiu, Z. / Yedidi, R.S. / Wang, Y. / Dewdney, T. / Reiter, S. / Brunzelle, J. / Kovari, I. / Kovari, L.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2013
Title: Crystallographic study of multi-drug resistant HIV-1 protease lopinavir complex: mechanism of drug recognition and resistance.
Authors: Liu, Z. / Yedidi, R.S. / Wang, Y. / Dewdney, T.G. / Reiter, S.J. / Brunzelle, J.S. / Kovari, I.A. / Kovari, L.C.
History
DepositionJun 3, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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

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Assembly

Deposited unit
A: MDR769 HIV-1 protease
B: MDR769 HIV-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,1703
Polymers21,5412
Non-polymers6291
Water3,999222
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
ΔGint-16 kcal/mol
Surface area9830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)43.828, 43.828, 101.805
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 MDR769 HIV-1 protease


Mass: 10769.635 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: Q000H7
#2: Protein MDR769 HIV-1 protease


Mass: 10771.607 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: Q000H7
#3: Chemical ChemComp-AB1 / N-{1-BENZYL-4-[2-(2,6-DIMETHYL-PHENOXY)-ACETYLAMINO]-3-HYDROXY-5-PHENYL-PENTYL}-3-METHYL-2-(2-OXO-TETRAHYDRO-PYRIMIDIN-1-YL)-BUTYRAMIDE / ABT-378 / LOPINAVIR


Mass: 628.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C37H48N4O5 / Comment: antiretroviral, protease inhibitor*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.27 Å3/Da / Density % sol: 45.8 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.6
Details: The hanging drop vapor diffusion method was used to form the bipyramidal crystals of the MDR 769 protease. Using a grid screen consisting of sodium chloride (0.7 to 1.4 M) and MES-HEPES ...Details: The hanging drop vapor diffusion method was used to form the bipyramidal crystals of the MDR 769 protease. Using a grid screen consisting of sodium chloride (0.7 to 1.4 M) and MES-HEPES buffer (pH 5.5 to 8.1), the HIV-1 protease substrate complex crystals formed overnight at 22 C. Routinely, 0.2 mm crystals, in the longest dimension, were obtained after 14 days of incubation. In each well, there were two droplets, containing 1 lL of protease substrate mixture, 1 lL of reservoir solution and 2 lL of protease substrate mixture, 1 lL of reservoir solution, respectively, 07 mL of well solution., VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 21, 2008
RadiationMonochromator: Ni MIRROR + Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.9→43.81 Å / Num. obs: 14375

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Processing

Software
NameVersionClassification
HKL-2000data collection
MOLREPphasing
REFMAC5.2.0019refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→43.81 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.894 / SU B: 3.712 / SU ML: 0.113 / Cross valid method: THROUGHOUT / ESU R: 0.189 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26003 765 5.1 %RANDOM
Rwork0.19748 ---
obs0.2006 14375 99.92 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.672 Å2
Baniso -1Baniso -2Baniso -3
1-0.4 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.79 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 46 222 1782
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0221591
X-RAY DIFFRACTIONr_angle_refined_deg1.8152.012164
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0655196
X-RAY DIFFRACTIONr_dihedral_angle_2_deg42.4952556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.46215272
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.836158
X-RAY DIFFRACTIONr_chiral_restr0.0850.2257
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.021161
X-RAY DIFFRACTIONr_nbd_refined0.2240.21057
X-RAY DIFFRACTIONr_nbtor_refined0.3380.21130
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1550.2261
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2350.295
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1830.238
X-RAY DIFFRACTIONr_mcbond_it0.9951.5992
X-RAY DIFFRACTIONr_mcangle_it1.69921600
X-RAY DIFFRACTIONr_scbond_it2.2843660
X-RAY DIFFRACTIONr_scangle_it3.7384.5564
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.246 54 -
Rwork0.209 1066 -
obs--100 %

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