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- PDB-3qro: HIV-1 protease (mutant Q7K L33I L63I) in complex with a three-arm... -

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Basic information

Entry
Database: PDB / ID: 3qro
TitleHIV-1 protease (mutant Q7K L33I L63I) in complex with a three-armed pyrrolidine-based inhibitor
ComponentsProtease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Aspartyl Protease / 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 / symbiont-mediated suppression of host gene expression / viral penetration into host nucleus / 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 / RNase H type-1 domain profile. / Ribonuclease H domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Reverse transcriptase domain / Reverse transcriptase (RT) catalytic domain profile. / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Reverse transcriptase (RNA-dependent DNA polymerase) / Retroviral matrix protein / Retrovirus capsid, C-terminal / 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
DITHIANE DIOL / Chem-NK9 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.616 Å
AuthorsLindemann, I. / Heine, A. / Klebe, G.
CitationJournal: To be Published
Title: Design of a series of novel three-armed pyrrolidine-based inhibitors for HIV-1 protease
Authors: Lindemann, I. / Klee, N. / Heine, A. / Diederich, W.E. / Klebe, G.
History
DepositionFeb 18, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 22, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._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

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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)22,5258
Polymers21,6102
Non-polymers9156
Water3,711206
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-24 kcal/mol
Surface area9750 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.410, 86.280, 46.240
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Protease / PR / Retropepsin


Mass: 10804.808 Da / Num. of mol.: 2 / Mutation: Q7K L33I L63I
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 (BRU ISOLATE)
Plasmid: pET24a / Production host: Escherichia coli (E. coli) / References: UniProt: P03367, HIV-1 retropepsin

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Non-polymers , 5 types, 212 molecules

#2: Chemical ChemComp-NK9 / 4-({(3S,4S)-4-[(3,5-dihydroxybenzyl)amino]pyrrolidin-3-yl}[4-(trifluoromethyl)benzyl]sulfamoyl)benzamide


Mass: 564.577 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C26H27F3N4O5S
#3: Chemical ChemComp-DTD / DITHIANE DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 206 / 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: 2.65 Å3/Da / Density % sol: 53.58 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 700mM NaCl, 100mM Na citrate pH 5.5, 100mM DTT, 3mM NaN3, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.2 / Wavelength: 0.91841 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Jun 25, 2010 / Details: mirrors
RadiationMonochromator: Double Crystal Monochromator KMC-2 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91841 Å / Relative weight: 1
ReflectionResolution: 1.616→30 Å / Num. all: 29643 / Num. obs: 29642 / % possible obs: 100 % / Redundancy: 5.1 % / Biso Wilson estimate: 14.62 Å2 / Rsym value: 0.061 / Net I/σ(I): 25.5
Reflection shellResolution: 1.62→1.65 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 1251 / Rsym value: 0.357 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2PQZ

2pqz


Resolution: 1.616→23.468 Å / Occupancy max: 1 / Occupancy min: 0.2 / SU ML: 0.16 / σ(F): 0 / Phase error: 18.59 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1932 2869 9.97 %random
Rwork0.1756 ---
obs0.1774 28787 95.56 %-
all-28787 --
Solvent computationShrinkage radii: 0.95 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 42.909 Å2 / ksol: 0.373 e/Å3
Displacement parametersBiso max: 63.18 Å2 / Biso mean: 18.0751 Å2 / Biso min: 5.16 Å2
Baniso -1Baniso -2Baniso -3
1-1.9865 Å2-0 Å2-0 Å2
2---0.5435 Å20 Å2
3----1.443 Å2
Refinement stepCycle: LAST / Resolution: 1.616→23.468 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1506 0 56 206 1768
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0081678
X-RAY DIFFRACTIONf_angle_d1.332302
X-RAY DIFFRACTIONf_chiral_restr0.225279
X-RAY DIFFRACTIONf_plane_restr0.006282
X-RAY DIFFRACTIONf_dihedral_angle_d17.101660
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.6164-1.67410.26322240.23542068229277
1.6741-1.74110.26992580.21212433269191
1.7411-1.82040.21192640.18642560282495
1.8204-1.91630.20942800.18132594287496
1.9163-2.03630.19483040.16992624292898
2.0363-2.19340.19723240.17142630295499
2.1934-2.41390.22762870.18312696298399
2.4139-2.76280.22093070.1812691299899
2.7628-3.4790.18292970.174827523049100
3.479-23.47090.15183240.159328703194100

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