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- PDB-1kzk: JE-2147-HIV Protease Complex -

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Basic information

Entry
Database: PDB / ID: 1kzk
TitleJE-2147-HIV Protease Complex
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HIV Protease Complex / Anisotropic Displacement Parameters / Viral protein / hydrolase / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / host multivesicular body / RNA-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / host cell / viral nucleocapsid / DNA recombination / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase activity / symbiont-mediated suppression of host gene expression / viral translational frameshifting / lipid binding / symbiont entry into host cell / 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. / 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. / Peptidase A2A, retrovirus, catalytic / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retroviral matrix protein / Cathepsin D, subunit A; domain 1 / Acid Proteases / Retrovirus capsid, N-terminal / 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
KNI-764 / Chem-JE2 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.09 Å
AuthorsReiling, K.K. / Endres, N.F. / Dauber, D.S. / Craik, C.S. / Stroud, R.M.
Citation
Journal: Biochemistry / Year: 2002
Title: Anisotropic Dynamics of the JE-2147-HIV Protease Complex: Drug Resistance and Thermodynamic Binding Mode Examined in a 1.09 A Structure
Authors: Reiling, K.K. / Endres, N.F. / Dauber, D.S. / Craik, C.S. / Stroud, R.M.
#1: Journal: J.Med.Chem. / Year: 1999
Title: Structure-Activity Relationship of Small-Sized HIV Protease Inhibitors Containing Allophenylnorstatine
Authors: Mimoto, T. / Kato, R. / Takaku, H. / Nojima, S. / Terashima, K. / Misawa, S. / Fukazawa, T. / Ueno, T. / Sato, H. / Shintani, M. / Kiso, Y. / Hayashi, H.
History
DepositionFeb 6, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 3, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: 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 1.3Dec 12, 2012Group: Other
Revision 1.4Jan 24, 2018Group: Database references / Category: citation_author / Item: _citation_author.name
Revision 1.5Oct 27, 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 1.6Aug 16, 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

Downloads & links

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Assembly

Deposited unit
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,66713
Polymers21,6042
Non-polymers1,06311
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5980 Å2
ΔGint-61 kcal/mol
Surface area9880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.203, 58.409, 62.858
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
DetailsThe Protease is active as a Dimer

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Components

#1: Protein Protease / Retropepsin


Mass: 10801.763 Da / Num. of mol.: 2 / Mutation: Q7K, K14R, S37N, R41K, L63P, I64V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus / Genus: Lentivirus / Plasmid: pTacTac / Production host: Escherichia coli (E. coli) / References: UniProt: P03369, HIV-1 retropepsin
#2: Chemical ChemComp-JE2 / (4R)-3-{(2S,3S)-2-hydroxy-3-[(3-hydroxy-2-methylbenzoyl)amino]-4-phenylbutanoyl}-5,5-dimethyl-N-(2-methylbenzyl)-1,3-thiazolidine-4-carboxamide / JE-2147 / AG1776 / KNI-764


Type: peptide-like, Peptide-like / Class: Enzyme inhibitor / Mass: 575.718 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C32H37N3O5S / References: KNI-764
#3: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 223 / 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: 2.18 Å3/Da / Density % sol: 43.46 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: NaAc, NaCl, EDTA, DTT, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 25 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
120 mM1droppH5.4NaAc
250 mM1dropNaCl
31 mMEDTA1drop
41 mMdithiothreitol1drop
50.200 mMprotein1drop
61.5 M1reservoirNaCl
720 mM1reservoirpH7.0NaAc
81 mMEDTA1reservoir
91 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 110 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.98 Å
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Mar 9, 2000
RadiationMonochromator: single crystal Si(311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.09→42.64 Å / Num. all: 79223 / Num. obs: 79223 / % possible obs: 93.3 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 5.5 % / Biso Wilson estimate: 6.4 Å2 / Rmerge(I) obs: 0.102 / Net I/σ(I): 10.5
Reflection shellResolution: 1.09→1.11 Å / Rmerge(I) obs: 0.717 / Mean I/σ(I) obs: 1.1 / % possible all: 61.8
Reflection
*PLUS
Highest resolution: 1.09 Å / Lowest resolution: 42.64 Å / % possible obs: 93.4 % / Num. measured all: 433956 / Rmerge(I) obs: 0.104
Reflection shell
*PLUS
Lowest resolution: 3.15 Å / % possible obs: 61.8 % / Rmerge(I) obs: 0.753

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Processing

Software
NameClassification
AMoREphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: Poly Serine PDB ENTRY 1HPX

1hpx


Resolution: 1.09→6 Å / Num. parameters: 16580 / Num. restraintsaints: 21599 / Cross valid method: Free-R / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1885 2251 3.1 %RANDOM
Rwork0.1506 ---
all0.152 73360 --
obs0.152 73360 93.3 %-
Displacement parametersBiso mean: 12.9 Å2
Refine analyzeNum. disordered residues: 12 / Occupancy sum hydrogen: 1506.94 / Occupancy sum non hydrogen: 1771.55
Refinement stepCycle: LAST / Resolution: 1.09→6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1508 0 66 223 1797
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.035
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0301
X-RAY DIFFRACTIONs_zero_chiral_vol0.079
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.084
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.047
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.075
X-RAY DIFFRACTIONs_approx_iso_adps0.113
LS refinement shell
Resolution (Å)Rfactor RworkRefine-IDNum. reflection obs% reflection obs (%)
1.09-1.150.27X-RAY DIFFRACTION794268.91
1.15-1.230.27X-RAY DIFFRACTION1079088.44
1.23-1.330.27X-RAY DIFFRACTION1122298.18
1.33-1.480.27X-RAY DIFFRACTION1187899.89
1.48-1.730.27X-RAY DIFFRACTION11827100
1.73-60.27X-RAY DIFFRACTION1970299.88
Software
*PLUS
Name: SHELXL / Version: 97 / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS

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