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- PDB-1izh: Inhibitor of HIV protease with unusual binding mode potently inhi... -

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Basic information

Entry
Database: PDB / ID: 1izh
TitleInhibitor of HIV protease with unusual binding mode potently inhibiting multi-resistant protease mutants
Componentsproteinase
KeywordsHYDROLASE / HIV-1 proteinase / potent inhibitor / subsite binding
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Retropepsin-like catalytic domain / 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 ...Retropepsin-like catalytic domain / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.9 Å
AuthorsWeber, J. / Mesters, J.R. / Lepsik, M. / Prejdova, J. / Svec, M. / Sponarova, J. / Mlcochova, P. / Skalicka, K. / Strisovsky, K. / Uhlikova, T. ...Weber, J. / Mesters, J.R. / Lepsik, M. / Prejdova, J. / Svec, M. / Sponarova, J. / Mlcochova, P. / Skalicka, K. / Strisovsky, K. / Uhlikova, T. / Soucek, M. / Machala, L. / Stankova, M. / Vondrasek, J. / Klimkait, T. / Kraeusslich, H.-G. / Hilgenfeld, R. / Konvalinka, J.
CitationJournal: J.MOL.BIOL. / Year: 2002
Title: Unusual Binding Mode of an HIV-1 Protease Inhibitor Explains its Potency against Multi-drug-resistant Virus Strains
Authors: Weber, J. / Mesters, J.R. / Lepsik, M. / Prejdova, J. / Svec, M. / Sponarova, J. / Mlcochova, P. / Skalicka, K. / Strisovsky, K. / Uhlikova, T. / Soucek, M. / Machala, L. / Stankova, M. / ...Authors: Weber, J. / Mesters, J.R. / Lepsik, M. / Prejdova, J. / Svec, M. / Sponarova, J. / Mlcochova, P. / Skalicka, K. / Strisovsky, K. / Uhlikova, T. / Soucek, M. / Machala, L. / Stankova, M. / Vondrasek, J. / Klimkait, T. / Kraeusslich, H.-G. / Hilgenfeld, R. / Konvalinka, J.
History
DepositionOct 2, 2002Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 25, 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: proteinase
B: proteinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3473
Polymers21,6622
Non-polymers6861
Water3,981221
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5190 Å2
ΔGint-26 kcal/mol
Surface area9270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.452, 85.756, 46.746
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
DetailsThe biological assembly is the homodimer as found in the asymmetric unit

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Components

#1: Protein proteinase / protease


Mass: 10830.781 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Plasmid: pET24a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q90EB9, HIV-1 retropepsin
#2: Chemical ChemComp-Q50 / {(1S)-1-BENZYL-4-[3-CARBAMOYL-1-(1-CARBAMOYL-2-PHENYL-ETHYLCARBAMOYL)-(S)-PROPYLCARBAMOYL]-2-OXO-5-PHENYL-PENTYL}-CARBAMIC ACID TERT-BUTYL ESTER


Mass: 685.809 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H47N5O7
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 221 / 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: 2.7 Å3/Da / Density % sol: 54.49 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 6
Details: MES, DTT, EDTA, NaN3, KCl, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 278K
Crystal grow
*PLUS
Temperature: 4 ℃ / pH: 6
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
125 mMMES1droppH6.0
210 %(v/v)glycerol1drop
31 mMEDTA1drop
41 mMdithiothreitol1drop
52-5 mg/mlprotein1drop
60.7-1.0 M1reservoirKCl
7100 mMMES1reservoirpH6.0
83 mM1reservoirNaN3
910 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: ENRAF-NONIUS FR591 / Wavelength: 1.54178 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Jul 1, 1997
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54178 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. all: 18388 / Num. obs: 18388 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.74 % / Biso Wilson estimate: 22.772 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 12.3
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.376 / Mean I/σ(I) obs: 3 / Num. unique all: 1715 / % possible all: 91.3
Reflection
*PLUS
Highest resolution: 1.9 Å

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
REFMAC- FOURIER SYNTHESISrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 5HVP

5hvp


Resolution: 1.9→43.03 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.917 / SU B: 3.312 / SU ML: 0.098 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.149 / ESU R Free: 0.154 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2408 948 5.2 %RANDOM
Rwork0.17808 ---
all0.18116 18388 --
obs0.18116 17421 95.89 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 23.734 Å2
Baniso -1Baniso -2Baniso -3
1-0.7 Å20 Å20 Å2
2---0.66 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.9→43.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1520 0 100 221 1841
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0220.0221650
X-RAY DIFFRACTIONr_bond_other_d0.0010.021598
X-RAY DIFFRACTIONr_angle_refined_deg1.7272.0462234
X-RAY DIFFRACTIONr_angle_other_deg0.73633712
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6445196
X-RAY DIFFRACTIONr_chiral_restr0.1110.2262
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021762
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02310
X-RAY DIFFRACTIONr_nbd_refined0.1890.3290
X-RAY DIFFRACTIONr_nbd_other0.2750.31857
X-RAY DIFFRACTIONr_nbtor_other0.090.5985
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1990.5251
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.0960.35
X-RAY DIFFRACTIONr_symmetry_vdw_other0.260.344
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.512
X-RAY DIFFRACTIONr_mcbond_it1.6132976
X-RAY DIFFRACTIONr_mcangle_it2.48931584
X-RAY DIFFRACTIONr_scbond_it1.9382674
X-RAY DIFFRACTIONr_scangle_it3.0483650
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.297 74
Rwork0.221 1196
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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