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- PDB-1iiq: CRYSTAL STRUCTURE OF HIV-1 PROTEASE COMPLEXED WITH A HYDROXYETHYL... -

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Basic information

Entry
Database: PDB / ID: 1iiq
TitleCRYSTAL STRUCTURE OF HIV-1 PROTEASE COMPLEXED WITH A HYDROXYETHYLAMINE PEPTIDOMIMETIC INHIBITOR
ComponentsPROTEASE RETROPEPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV protease / peptidomimetics / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / symbiont-mediated suppression of host gene expression / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / lipid binding / host cell nucleus / host cell plasma membrane / structural molecule activity / virion membrane / proteolysis / DNA binding / zinc ion binding / membrane
Similarity search - Function
Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain ...Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Integrase Zinc binding domain / Zinc finger integrase-type profile. / Integrase-like, N-terminal / Integrase DNA binding domain / Integrase, C-terminal domain superfamily, retroviral / Integrase, N-terminal zinc-binding domain / Integrase, C-terminal, retroviral / Integrase DNA binding domain profile. / Immunodeficiency lentiviral matrix, N-terminal / gag gene protein p17 (matrix protein) / RNase H / Integrase core domain / Integrase, catalytic core / Integrase catalytic domain profile. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / 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 / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type superfamily / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Ribonuclease H superfamily / Aspartic peptidase domain superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BOC-PS0-PHE-GLN-PHE-NH2 / Chem-0ZR / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.83 Å
AuthorsDohnalek, J. / Hasek, J. / Duskova, J. / Petrokova, H. / Hradilek, M. / Soucek, M. / Konvalinka, J. / Brynda, J. / Sedlacek, J. / Fabry, M.
Citation
Journal: J.Med.Chem. / Year: 2002
Title: Hydroxyethylamine isostere of an HIV-1 protease inhibitor prefers its amine to the hydroxy group in binding to catalytic aspartates. A synchrotron study of HIV-1 protease in complex with a ...Title: Hydroxyethylamine isostere of an HIV-1 protease inhibitor prefers its amine to the hydroxy group in binding to catalytic aspartates. A synchrotron study of HIV-1 protease in complex with a peptidomimetic inhibitor.
Authors: Dohnalek, J. / Hasek, J. / Duskova, J. / Petrokova, H. / Hradilek, M. / Soucek, M. / Konvalinka, J. / Brynda, J. / Sedlacek, J. / Fabry, M.
#1: Journal: Acta Crystallogr.,Sect.D / Year: 2001
Title: A distinct binding mode of a hydroxyethylamine isostere inhibitor of HIV-1 protease
Authors: Dohnalek, J. / Hasek, J. / Duskova, J. / Petrokova, H. / Hradilek, M. / Soucek, M. / Konvalinka, J. / Brynda, J. / Sedlacek, J. / Fabry, M.
History
DepositionApr 24, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 12, 2002Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Oct 4, 2017Group: Advisory / Refinement description / Category: pdbx_unobs_or_zero_occ_atoms / software / Item: _software.name
Revision 1.5Aug 16, 2023Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / 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
Revision 1.6Mar 13, 2024Group: Source and taxonomy / Structure summary / Category: entity / pdbx_entity_src_syn / Item: _entity.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEASE RETROPEPSIN
B: PROTEASE RETROPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7718
Polymers21,6082
Non-polymers1,1636
Water5,423301
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)58.110, 86.340, 46.110
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Cell settingorthorhombic
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-523-

HOH

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Components

#1: Protein PROTEASE RETROPEPSIN / E.C.3.4.23.16 / HIV-1 PROTEASE


Mass: 10803.756 Da / Num. of mol.: 2 / Fragment: HIV-1 PROTEASE
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: P03367, HIV-1 retropepsin
#2: Chemical ChemComp-0ZR / N-{(2R,3S)-3-[(tert-butoxycarbonyl)amino]-2-hydroxy-4-phenylbutyl}-L-phenylalanyl-L-glutaminyl-L-phenylalaninamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 702.840 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H50N6O7 / Details: peptidomimetic inhibitor / References: BOC-PS0-PHE-GLN-PHE-NH2
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 301 / 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: 2

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Sample preparation

CrystalDensity Matthews: 2.59 Å3/Da / Density % sol: 52.56 %
Crystal growTemperature: 280 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: ammonium phosphate, sodium citrate, pH 4.5, VAPOR DIFFUSION, HANGING DROP at 280K
Crystal grow
*PLUS
Details: Jancarik, J., (1991) J. Appl. Crystallogr., 24, 409., Dohnalek, J., (1998) Gen. Physiol. Biophys., 17, Suppl. 1, 9., Buchtelova, E., (1999) Mater. Struct., 6, 6.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 10, 1997
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.83→11 Å / Num. all: 20474 / Num. obs: 20474 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.2 % / Biso Wilson estimate: 5.8 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.8
Reflection shellResolution: 1.83→1.88 Å / Rmerge(I) obs: 0.22 / Mean I/σ(I) obs: 4.9 / Num. unique all: 1382 / % possible all: 93.7
Reflection
*PLUS
Num. measured all: 188100 / Rmerge(I) obs: 0.11
Reflection shell
*PLUS
% possible obs: 93.7 % / Num. measured obs: 1392 / Rmerge(I) obs: 0.22

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Processing

Software
NameVersionClassification
AMoREphasing
CNS1refinement
XDSdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1HSG

1hsg


Resolution: 1.83→10.91 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 1339622.94 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
Stereochemistry target values: Engh & Huber, ligand parametrisation: CSD structural database
Details: Used maximum likelihood and conjugated gradient least squares refinement.
RfactorNum. reflection% reflectionSelection details
Rfree0.204 1002 4.9 %RANDOM
Rwork0.164 ---
obs0.164 20446 97.2 %-
all-21035 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 87.55 Å2 / ksol: 0.471 e/Å3
Displacement parametersBiso mean: 14.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.2 Å0.16 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.83→10.91 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 81 301 1898
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d25.6
X-RAY DIFFRACTIONc_improper_angle_d0.95
X-RAY DIFFRACTIONc_mcbond_it2.053
X-RAY DIFFRACTIONc_mcangle_it2.863
X-RAY DIFFRACTIONc_scbond_it3.014
X-RAY DIFFRACTIONc_scangle_it4.44
LS refinement shellResolution: 1.83→1.94 Å / Rfactor Rfree error: 0.018 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.226 165 5 %
Rwork0.177 3157 -
obs-3322 96.6 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAWATER.TOP
X-RAY DIFFRACTION3INH_ALL.PARINH_ALL_FREEBOC.TOP
Refinement
*PLUS
% reflection Rfree: 5 % / Rfactor obs: 0.17 / Rfactor Rfree: 0.21 / Rfactor Rwork: 0.17
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.51
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg25.6
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.95
LS refinement shell
*PLUS
Rfactor Rfree: 0.226 / Rfactor Rwork: 0.177

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