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- PDB-2pk5: Crystal Structure of HIV-1 Protease (Q7K, L33I, L63I ) in Complex... -

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Basic information

Entry
Database: PDB / ID: 2pk5
TitleCrystal Structure of HIV-1 Protease (Q7K, L33I, L63I ) in Complex with KNI-10075
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / PROTEASE COMPLEX / Viral Protein / 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 / host multivesicular body / DNA integration / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency ...HIV-1 retropepsin / symbiont-mediated activation of host apoptosis / 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 / symbiont-mediated suppression of host gene expression / RNA stem-loop binding / 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 / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / viral translational frameshifting / 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. / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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. / 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-10075 / Chem-075 / Gag-Pol polyprotein / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsArmstrong, A.A. / Lafont, V. / Kiso, Y. / Freire, E. / Amzel, L.M.
CitationJournal: Chem.Biol.Drug Des. / Year: 2007
Title: Compensating enthalpic and entropic changes hinder binding affinity optimization.
Authors: Lafont, V. / Armstrong, A.A. / Ohtaka, H. / Kiso, Y. / Mario Amzel, L. / Freire, E.
History
DepositionApr 17, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 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 1.4Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.5Oct 20, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _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 30, 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)22,5064
Polymers21,6102
Non-polymers8962
Water4,342241
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-30 kcal/mol
Surface area9340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.842, 85.991, 46.210
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: 10804.808 Da / Num. of mol.: 2 / Mutation: Q7K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: SUBTYPE B / Gene: gag-pol / Plasmid: pET24a+ / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03367, UniProt: Q9J2P7*PLUS
#2: Chemical ChemComp-075 / (4R)-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-3-[(2S,3S)-2-hydroxy-3-({N-[(isoquinolin-5-yloxy)acetyl]-3-(methyl sulfonyl)-L-alanyl}amino)-4-phenylbutanoyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide / KNI-10075


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 803.943 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C40H45N5O9S2 / References: KNI-10075
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 241 / 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: 2.7 Å3/Da / Density % sol: 54.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: 100 mM citrate buffer pH 5.4, NaCl 750 mM, 10 mM DTT, 3 mM NaN3, VAPOR DIFFUSION, HANGING DROP, temperature 298KK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 27, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1 Å / Relative weight: 1
ReflectionResolution: 1.9→50 Å / Num. obs: 19013 / % possible obs: 99.8 % / Redundancy: 6 % / Rmerge(I) obs: 0.113 / Rsym value: 0.113 / Χ2: 5.306 / Net I/σ(I): 14.2
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.415 / Mean I/σ(I) obs: 8.63 / Num. unique all: 1856 / Rsym value: 0.415 / Χ2: 3.78 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MSM

1msm


Resolution: 1.9→48.56 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.947 / SU B: 5.192 / SU ML: 0.081 / Cross valid method: THROUGHOUT / ESU R: 0.143 / ESU R Free: 0.133 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2 1940 10.2 %RANDOM
Rwork0.16 ---
obs0.164 18976 99.72 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.898 Å2
Baniso -1Baniso -2Baniso -3
1--0.26 Å20 Å20 Å2
2--0 Å20 Å2
3---0.26 Å2
Refinement stepCycle: LAST / Resolution: 1.9→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 62 241 1819
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221722
X-RAY DIFFRACTIONr_angle_refined_deg1.5912.0672348
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2765204
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.08924.71753
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.63315300
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.876158
X-RAY DIFFRACTIONr_chiral_restr0.1020.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021230
X-RAY DIFFRACTIONr_nbd_refined0.2050.2772
X-RAY DIFFRACTIONr_nbtor_refined0.3130.21178
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2170
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.244
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1080.215
X-RAY DIFFRACTIONr_mcbond_it0.9521.51090
X-RAY DIFFRACTIONr_mcangle_it1.29421667
X-RAY DIFFRACTIONr_scbond_it2.1833757
X-RAY DIFFRACTIONr_scangle_it3.1664.5681
LS refinement shellResolution: 1.903→1.952 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.226 156 -
Rwork0.165 1196 -
obs-1352 98.11 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9441-0.2948-0.48690.98240.38691.1740.0194-0.09340.03550.07060.0178-0.0501-0.05690.0963-0.03710.02480.0027-0.0145-0.0340.0011-0.103814.657-11.288-10.08
20.411-0.6777-0.27321.74220.51890.9764-0.02590.0181-0.0165-0.05780.03370.0414-0.0217-0.0063-0.00780.0049-0.0038-0.0032-0.0310.0065-0.095516.499-22.301-28.647
31.8195-3.5304-2.069913.33640.63324.11930.07880.12-0.3766-0.151-0.22670.50150.0314-0.15660.1479-0.05250.0126-0.0125-0.06350.0084-0.1512.775-20.878-17.121
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 991 - 99
22BB1 - 991 - 99
33AC900

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