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- PDB-1zj7: Crystal structure of a complex of mutant HIV-1 protease (A71V, V8... -

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Basic information

Entry
Database: PDB / ID: 1zj7
TitleCrystal structure of a complex of mutant HIV-1 protease (A71V, V82T, I84V) with a hydroxyethylamine peptidomimetic inhibitor BOC-PHE-PSI[S-CH(OH)CH2NH]-PHE-GLU-PHE-NH2
ComponentsPROTEASE RETROPEPSIN
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV / PROTEASE / PEPTIDOMIMETIC INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX
Function / homology
Function and homology information


RNA stem-loop binding / host cell / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase ...RNA stem-loop binding / host cell / HIV-1 retropepsin / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / virion membrane / structural molecule activity / 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 / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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-PHE-PSI[S-CH(OH)CH2NH]-PHE-GLU-PHE-NH2 / Chem-0ZT / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.93 Å
AuthorsSkalova, T. / Dohnalek, J. / Duskova, J. / Petrokova, H. / Hasek, J.
CitationJournal: J.Med.Chem. / Year: 2006
Title: HIV-1 protease mutations and inhibitor modifications monitored on a series of complexes. Structural basis for the effect of the A71V mutation on the active site
Authors: Skalova, T. / Dohnalek, J. / Duskova, J. / Petrokova, H. / Hradilek, M. / Soucek, M. / Konvalinka, J. / Hasek, J.
History
DepositionApr 28, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 9, 2006Provider: 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 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Dec 12, 2012Group: Other
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations
Category: database_2 / struct_ref_seq_dif ...database_2 / struct_ref_seq_dif / struct_sheet / 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_sheet.number_strands / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.6Aug 23, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEASE RETROPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,5242
Polymers10,8201
Non-polymers7041
Water1,11762
1
A: PROTEASE RETROPEPSIN
hetero molecules

A: PROTEASE RETROPEPSIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)23,0474
Polymers21,6402
Non-polymers1,4082
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+2/31
Buried area7180 Å2
ΔGint-29 kcal/mol
Surface area8860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.859, 62.859, 83.253
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number178
Cell settinghexagonal
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-301-

HOH

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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.: 1 / Mutation: A71V, V82T, I84V
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(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03367, HIV-1 retropepsin
#2: Chemical ChemComp-0ZT / N-{(2S,3S)-3-[(tert-butoxycarbonyl)amino]-2-hydroxy-4-phenylbutyl}-L-phenylalanyl-L-alpha-glutamyl-L-phenylalaninamide


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 703.824 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H49N5O8 / References: BOC-PHE-PSI[S-CH(OH)CH2NH]-PHE-GLU-PHE-NH2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 62 / 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: 1.94 Å3/Da / Density % sol: 36.11 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.4
Details: 0.1 M Na Citrate, 0.5 M NaCl, 10% (v/v) glycerol, pH 4.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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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 / Details: microfocusing mirrors - testing
RadiationMonochromator: Diamond C 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.93→20 Å / Num. all: 6784 / Num. obs: 6784 / % possible obs: 87.6 % / Observed criterion σ(I): -999 / Redundancy: 6.7 % / Biso Wilson estimate: 36.7 Å2 / Rmerge(I) obs: 0.048 / Rsym value: 0.048 / Net I/σ(I): 28.1
Reflection shellResolution: 1.93→2 Å / Redundancy: 6.5 % / Rmerge(I) obs: 0.434 / Mean I/σ(I) obs: 4.4 / Num. unique all: 627 / Rsym value: 0.434 / % possible all: 85.4

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1IIQ

1iiq


Resolution: 1.93→20 Å / Data cutoff high absF: 10000 / Data cutoff low absF: 0 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Used maximum likelihood refinement procedure on amplitudes and least squares residual on amplitudes.
RfactorNum. reflection% reflectionSelection details
Rfree0.2994 355 5.3 %RANDOM
Rwork0.2288 ---
all0.2287 6714 --
obs0.2287 6714 86.41 %-
Solvent computationSolvent model: AS IMPLEMENTED IN CNS 1.1 / Bsol: 78.09 Å2 / ksol: 0.337 e/Å3
Displacement parametersBiso mean: 33.7 Å2
Baniso -1Baniso -2Baniso -3
1-0.046 Å22.091 Å20 Å2
2--0.046 Å20 Å2
3----0.092 Å2
Refine analyzeLuzzati coordinate error obs: 0.307 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 1.93→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms759 0 51 62 872
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.012411
X-RAY DIFFRACTIONc_angle_deg1.70665
X-RAY DIFFRACTIONc_mcbond_it2.3162
X-RAY DIFFRACTIONc_scbond_it3.4423
X-RAY DIFFRACTIONc_mcangle_it3.8814
X-RAY DIFFRACTIONc_scangle_it5.2875
LS refinement shellResolution: 1.93→2.02 Å
RfactorNum. reflection
Rfree0.371 32
Rwork0.3574 -
obs-743

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