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- PDB-1lzq: Crystal structure of the complex of mutant HIV-1 protease (A71V, ... -

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Basic information

Entry
Database: PDB / ID: 1lzq
TitleCrystal structure of the complex of mutant HIV-1 protease (A71V, V82T, I84V) with an ethylenamine peptidomimetic inhibitor BOC-PHE-PSI[CH2CH2NH]-PHE-GLU-PHE-NH2
ComponentsPROTEASE RETROPEPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV / PEPTIDOMIMETIC / ethylenamine ISOSTERE / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA 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 / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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-PHE-PSI[CH2CH2NH]-PHE-GLU-PHE-NH2 / Chem-0ZQ / BETA-MERCAPTOETHANOL / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSkalova, T. / Hasek, J. / Dohnalek, J. / Petrokova, H. / Buchtelova, E. / Soucek, M. / Majer, P. / Uhlikova, T. / Konvalinka, J.
CitationJournal: J.Med.Chem. / Year: 2003
Title: An Ethylenamine Inhibitor Binds Tightly to Both Wild Type and Mutant HIV-1 Proteases. Structure and Energy Study
Authors: Skalova, T. / Hasek, J. / Dohnalek, J. / Petrokova, H. / Buchtelova, E. / Duskova, J. / Soucek, M. / Majer, P. / Uhlikova, T. / Konvalinka, J.
History
DepositionJun 11, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2003Provider: 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 / Source and taxonomy / Structure summary / Version format compliance
Revision 1.3Dec 12, 2012Group: Other
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations / Category: database_2 / 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
Revision 1.5Feb 14, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)22,4054
Polymers21,6402
Non-polymers7662
Water1,54986
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-22 kcal/mol
Surface area9040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.680, 62.680, 83.309
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Cell settinghexagonal
Space group name H-MP61
DetailsBIOLOGICAL ASSEMBLY IS A DIMER IN THE ASSYMETRIC UNIT

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Components

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


Mass: 10819.756 Da / Num. of mol.: 2 / Mutation: A71V, V82T, I84V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P03367, HIV-1 retropepsin
#2: Chemical ChemComp-0ZQ / N-{(3S)-3-[(tert-butoxycarbonyl)amino]-4-phenylbutyl}-L-phenylalanyl-L-alpha-glutamyl-L-phenylalaninamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 687.825 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H49N5O7 / References: BOC-PHE-PSI[CH2CH2NH]-PHE-GLU-PHE-NH2
#3: Chemical ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 86 / 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: 2.2 Å3/Da / Density % sol: 43.7 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: NaCl, GLYCEROL, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal grow
*PLUS
pH: 5.8 / Method: vapor diffusion
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
150 mMsodium acetate1droppH5.8
21 mMEDTA1drop
30.05 %beta-mercaptoethanol1drop
43 mg/mlprotein1drop
50.5 M1reservoirNaCl
60.1 Msodium acetate1reservoirpH4.4
710-15 %glycerol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 12, 2000
RadiationMonochromator: Diamond (111), Sagitally focusing Ge(220) and a multilayer
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.2→33 Å / Num. all: 9504 / Num. obs: 9492 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 31.8 Å2 / Rmerge(I) obs: 0.079
Reflection shellResolution: 2.2→2.26 Å / Rmerge(I) obs: 0.449 / Mean I/σ(I) obs: 3.3 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.2 Å / Num. obs: 9490 / Num. measured all: 61979

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→33 Å / Isotropic thermal model: ISOTROPIC / Cross valid method: THROUGHOUT EXCEPT LAST CYCLE / σ(F): 0 / Stereochemistry target values: CNS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 533 5.6 %RANDOM
Rwork0.203 ---
all0.208 9504 --
obs0.208 9492 99.9 %-
Displacement parametersBiso mean: 35 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.3 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.3 Å
Refinement stepCycle: LAST / Resolution: 2.2→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1518 0 54 86 1658
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_d1.6
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d26.47
X-RAY DIFFRACTIONc_improper_angle_d1.1
X-RAY DIFFRACTIONc_mcbond_it1.5981.5
X-RAY DIFFRACTIONc_mcangle_it2.6322
X-RAY DIFFRACTIONc_scbond_it2.2772
X-RAY DIFFRACTIONc_scangle_it3.4712.5
LS refinement shellResolution: 2.2→2.27 Å / Rfactor Rfree: 0.3176 / Rfactor Rwork: 0.2959 / Total num. of bins used: 10
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 33 Å / % reflection Rfree: 5.9 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_deg1.6
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg26.47
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg1.1

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