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- PDB-4fe6: Crystal Structure of HIV-1 Protease in Complex with an enamino-ox... -

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Basic information

Entry
Database: PDB / ID: 4fe6
TitleCrystal Structure of HIV-1 Protease in Complex with an enamino-oxindole inhibitor
ComponentsHIV proteaseHIV-1 protease
KeywordsHYDROLASE/INHIBITOR / 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 / RNA-directed DNA polymerase / viral genome integration into host DNA ...RNA stem-loop binding / host cell / 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 / 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
Chem-0TQ / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 2 Å
AuthorsSilva, A.M. / Eissenstat, M. / Guerassina, T. / Gulnik, S. / Afonina, E. / Yu, B. / Erickson, J. / Ludke, D. / Yokoe, H.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2012
Title: Enamino-oxindole HIV protease inhibitors.
Authors: Eissenstat, M. / Guerassina, T. / Gulnik, S. / Afonina, E. / Silva, A.M. / Ludtke, D. / Yokoe, H. / Yu, B. / Erickson, J.
History
DepositionMay 29, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 18, 2012Provider: repository / Type: Initial release
Revision 1.1Aug 1, 2012Group: Database references
Revision 1.2Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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

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Assembly

Deposited unit
A: HIV protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)11,4472
Polymers10,8041
Non-polymers6431
Water1,47782
1
A: HIV protease
hetero molecules

A: HIV protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,8934
Polymers21,6082
Non-polymers1,2862
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation9_555-x,-x+y,-z+2/31
Buried area4020 Å2
ΔGint-23 kcal/mol
Surface area9500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.654, 62.654, 82.361
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number178
Space group name H-MP6122
Components on special symmetry positions
IDModelComponents
11A-200-

0TQ

21A-3069-

HOH

31A-3079-

HOH

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Components

#1: Protein HIV protease / HIV-1 protease / PR / Retropepsin


Mass: 10803.756 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: BRU/LAI / Gene: gag-pol / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03367, HIV-1 retropepsin
#2: Chemical ChemComp-0TQ / (3R,3aS,6aR)-hexahydrofuro[2,3-b]furan-3-yl {(2S,3R)-3-hydroxy-4-[({(3Z)-3-[1-(methylamino)ethylidene]-2-oxo-2,3-dihydro-1H-indol-5-yl}sulfonyl)(2-methylpropyl)amino]-1-phenylbutan-2-yl}carbamate


Mass: 642.763 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H42N4O8S
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.16 Å3/Da / Density % sol: 43.05 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.6
Details: 0.3M AS, 5% ethanol, 5% methanol 10 mM DTT, pH 5.6, vapor diffusion, hanging drop, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.542 Å
DetectorType: RIGAKU RAXIS / Detector: IMAGE PLATE / Date: Nov 12, 2003 / Details: mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.542 Å / Relative weight: 1
ReflectionResolution: 2→40 Å / Num. obs: 6048 / % possible obs: 87 % / Rmerge(I) obs: 0.074 / Χ2: 2.091 / Net I/σ(I): 19
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2Diffraction-ID% possible all
2-2.070.2856401.709195.8
2.07-2.150.256481.965196.4
2.15-2.250.1973962.074158.8
2.25-2.370.1764552.354168.4
2.37-2.520.1446732.17197.7
2.52-2.710.1196682.324198.2
2.71-2.990.0966762.244198
2.99-3.420.0756852.202198
3.42-4.310.064412.183161.5
4.31-400.0557661.736196.5

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Processing

Software
NameVersionClassificationNB
SCALEPACKdata scaling
REFMAC5.6.0117refinement
PDB_EXTRACT3.11data extraction
StructureStudiodata collection
DENZOdata reduction
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 2→20.51 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.94 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 4.758 / SU ML: 0.127 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.246 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES: REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2608 282 4.7 %RANDOM
Rwork0.1802 ---
obs0.1838 6039 87.28 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 115.08 Å2 / Biso mean: 32.229 Å2 / Biso min: 14.41 Å2
Baniso -1Baniso -2Baniso -3
1--0.03 Å2-0.01 Å20 Å2
2---0.03 Å20 Å2
3---0.04 Å2
Refinement stepCycle: LAST / Resolution: 2→20.51 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms758 0 45 82 885
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.02833
X-RAY DIFFRACTIONr_angle_refined_deg2.7432.051135
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.2435100
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.34324.64328
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.88915143
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.753154
X-RAY DIFFRACTIONr_chiral_restr0.170.2133
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.021596
LS refinement shellResolution: 2→2.05 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.288 20 -
Rwork0.232 378 -
all-398 -
obs--94.76 %

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