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- PDB-3fx5: Structure of HIV-1 Protease in Complex with Potent Inhibitor KNI-... -

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Basic information

Entry
Database: PDB / ID: 3fx5
TitleStructure of HIV-1 Protease in Complex with Potent Inhibitor KNI-272 Determined by High Resolution X-ray Crystallography
Componentsprotease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / acid protease / homodimer / protease / Hydrolase / Nucleotidyltransferase / Transferase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


RNA-directed DNA polymerase activity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...RNA-directed DNA polymerase activity / HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / establishment of integrated proviral latency / viral penetration into host nucleus / telomerase activity / RNA stem-loop binding / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / endonuclease activity / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / viral translational frameshifting / 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 / 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 ...: / 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. / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / RNase H type-1 domain profile. / Ribonuclease H domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / Cathepsin D, subunit A; domain 1 / Acid Proteases / zinc finger / Zinc knuckle / 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. / Aspartic peptidase domain superfamily / Ribonuclease H superfamily / Ribonuclease H-like superfamily / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
kynostatin 272 / Chem-KNI / Gag-Pol polyprotein / Pol protein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 0.93 Å
AuthorsAdachi, M. / Ohhara, T. / Tamada, T. / Okazaki, N. / Kuroki, R.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2009
Title: Structure of HIV-1 protease in complex with potent inhibitor KNI-272 determined by high-resolution X-ray and neutron crystallography.
Authors: Adachi, M. / Ohhara, T. / Kurihara, K. / Tamada, T. / Honjo, E. / Okazaki, N. / Arai, S. / Shoyama, Y. / Kimura, K. / Matsumura, H. / Sugiyama, S. / Adachi, H. / Takano, K. / Mori, Y. / ...Authors: Adachi, M. / Ohhara, T. / Kurihara, K. / Tamada, T. / Honjo, E. / Okazaki, N. / Arai, S. / Shoyama, Y. / Kimura, K. / Matsumura, H. / Sugiyama, S. / Adachi, H. / Takano, K. / Mori, Y. / Hidaka, K. / Kimura, T. / Hayashi, Y. / Kiso, Y. / Kuroki, R.
History
DepositionJan 20, 2009Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Mar 24, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Nov 10, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / struct_ref_seq_dif / struct_site
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI ..._chem_comp.pdbx_synonyms / _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 1.4Nov 1, 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
B: protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,4256
Polymers21,4812
Non-polymers9444
Water8,467470
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5670 Å2
ΔGint-28 kcal/mol
Surface area9390 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)57.532, 85.955, 46.386
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-500-

HOH

21A-776-

HOH

31B-610-

HOH

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Components

#1: Protein protease


Mass: 10740.677 Da / Num. of mol.: 2 / Mutation: Q7K, L33I, L63I C67A, C95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pET43a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: Q9EKL4, UniProt: P03367*PLUS, HIV-1 retropepsin
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-KNI / (4R)-N-tert-butyl-3-[(2S,3S)-2-hydroxy-3-({N-[(isoquinolin-5-yloxy)acetyl]-S-methyl-L-cysteinyl}amino)-4-phenylbutanoyl]-1,3-thiazolidine-4-carboxamide / KNI-272 / (N-TERT-BUTYL-THIOPROLINE)-(5-ISOQUINOLYLOXYACETYL-METHYLTHIOALANINE)-ALLOPHENYLNORSTATINE


Type: peptide-like, Peptide-like / Class: Enzyme inhibitor / Mass: 667.839 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C33H41N5O6S2 / References: kynostatin 272
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 470 / 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: 2.67 Å3/Da / Density % sol: 53.93 %
Crystal growTemperature: 293 K / pH: 5
Details: 50mM citrate, 50mM Na-phosphate, 0.061M ammonium sulfate, pH 5.0, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.7085 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 15, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7085 Å / Relative weight: 1
ReflectionResolution: 0.93→47.2 Å / Num. obs: 150216 / % possible obs: 97.2 % / Redundancy: 7.7 % / Rmerge(I) obs: 0.062 / Net I/σ(I): 43.9
Reflection shellResolution: 0.93→0.96 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 3.2 / % possible all: 91.8

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Processing

Software
NameClassification
CNSrefinement
SHELXL-97refinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: PDB ENTRY 1HPX

1hpx


Resolution: 0.93→47.2 Å / σ(F): 0
RfactorNum. reflectionSelection details
Rfree0.124 7509 RANDOM
Rwork0.104 --
all-150216 -
obs-150216 -
Displacement parametersBiso max: 125.81 Å2 / Biso min: 3.55 Å2
Refinement stepCycle: LAST / Resolution: 0.93→47.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 64 470 2046
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.02
X-RAY DIFFRACTIONs_angle_d0.039

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