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- PDB-2zye: Structure of HIV-1 Protease in Complex with Potent Inhibitor KNI-... -

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Basic information

Entry
Database: PDB / ID: 2zye
TitleStructure of HIV-1 Protease in Complex with Potent Inhibitor KNI-272 Determined by Neutron Crystallography
Componentsprotease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV-1 protease / acid protease / homodimer / Hydrolase / Multifunctional enzyme / 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 / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / viral penetration into host nucleus ...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 / establishment of integrated proviral latency / viral penetration into host nucleus / RNA stem-loop binding / RNA-directed DNA polymerase activity / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / viral nucleocapsid / endonuclease activity / 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
kynostatin 272 / DEUTERATED WATER / Chem-KNI / Gag-Pol polyprotein / Pol protein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodNEUTRON DIFFRACTION / NUCLEAR REACTOR / Resolution: 1.9 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: PDBJ / 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 1.3Jun 20, 2018Group: Data collection / Category: diffrn_radiation / diffrn_source
Item: _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_source.pdbx_synchrotron_beamline ..._diffrn_radiation.pdbx_diffrn_protocol / _diffrn_source.pdbx_synchrotron_beamline / _diffrn_source.pdbx_synchrotron_site / _diffrn_source.source / _diffrn_source.type
Revision 1.4Nov 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 1.5May 29, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)22,1493
Polymers21,4812
Non-polymers6681
Water2,576143
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-26 kcal/mol
Surface area9960 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.500, 87.400, 46.800
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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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-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
#3: Chemical ChemComp-DOD / water


Mass: 18.015 Da / Num. of mol.: 143 / Source method: isolated from a natural source / Formula: D2O

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Experimental details

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Experiment

ExperimentMethod: NEUTRON DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 293 K / Method: macroseeding procedure, a two-liquid batch method / pH: 5
Details: 50mM citrate, 50mM Na-phosphate buffer, 0.061M ammonium sulfate, macroseeding procedure, a two-liquid batch method, temperature 293K, pH 5.0

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: NUCLEAR REACTOR / Site: JRR-3M / Beamline: 1G-A / Wavelength: 2.6 Å
DetectorType: neutron imaging plate / Detector: IMAGE PLATE / Date: Dec 26, 2008
RadiationMonochromator: elastically-bent perfect si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: neutron
Radiation wavelengthWavelength: 2.6 Å / Relative weight: 1
ReflectionResolution: 1.9→49.2 Å / Num. obs: 16632 / % possible obs: 83.6 % / Rmerge(I) obs: 0.073 / Net I/σ(I): 7.3
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.367 / Mean I/σ(I) obs: 1.7 / % possible all: 67.5

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Processing

Software
NameVersionClassification
PHENIX(phenix.refine)refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementResolution: 1.9→49.184 Å / SU ML: 0.24 / Phase error: 21.74 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.222 754 4.9 %
Rwork0.1925 --
obs0.194 15381 77.36 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 31.734 Å2 / ksol: 0.579 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-10.2175 Å20 Å20 Å2
2--5.9887 Å20 Å2
3---10.1392 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.184 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 46 143 1701
Refine LS restraints
Refine-IDTypeDev idealNumber
NEUTRON DIFFRACTIONf_bond_d0.0213741
NEUTRON DIFFRACTIONf_angle_d2.516639
NEUTRON DIFFRACTIONf_dihedral_angle_d23.23881
NEUTRON DIFFRACTIONf_chiral_restr0.156257
NEUTRON DIFFRACTIONf_plane_restr0.025666
LS refinement shell

Refine-ID: NEUTRON DIFFRACTION / Total num. of bins used: 5

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
1.9002-2.04690.29431240.2889228562
2.0469-2.25290.2861220.2339277174
2.2529-2.57890.20841460.1828300480
2.5789-3.2490.20691750.1657321086
3.249-49.20080.19621870.1731335785

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