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

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Basic information

Entry
Database: PDB / ID: 3qrm
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 / 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 / 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 / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / Retrovirus capsid, C-terminal / 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
DITHIANE DIOL / Chem-NK7 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.731 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)22,4697
Polymers21,6102
Non-polymers8595
Water4,504250
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3620 Å2
ΔGint-23 kcal/mol
Surface area9790 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.940, 86.030, 46.500
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 / 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
#2: Chemical ChemComp-NK7 / 4-{[4-(trifluoromethyl)benzyl][(3S,4S)-4-{[4-(trifluoromethyl)benzyl]amino}pyrrolidin-3-yl]sulfamoyl}benzamide


Mass: 600.576 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H26F6N4O3S
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-DTD / DITHIANE DIOL


Mass: 152.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H8O2S2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 250 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsNEXT TO THE DTD MOLECULE IN THE BINDING POCKET WE OBSERVED ADDITIONAL DENSITY (5.00 SIGMA LEVEL) ...NEXT TO THE DTD MOLECULE IN THE BINDING POCKET WE OBSERVED ADDITIONAL DENSITY (5.00 SIGMA LEVEL) WHICH COULD NOT BE SUFFICIENTLY EXPLAINED WITH ANY OF OUR CHEMICALS WE HAVE USED.

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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: 2.68 Å3/Da / Density % sol: 54.13 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 700mM NaCl, 100mM Na citrate, 100mM DTT, 3mM NaN3, pH 5.5, 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: Mar 26, 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: 1.73→30 Å / Num. all: 24130 / Num. obs: 24130 / % possible obs: 100 % / Redundancy: 3.6 % / Biso Wilson estimate: 13.59 Å2 / Rsym value: 0.044 / Net I/σ(I): 28.8
Reflection shellResolution: 1.73→1.76 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 6 / Num. unique all: 1150 / Rsym value: 0.19 / % 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: 1.731→25.701 Å / Occupancy max: 1 / Occupancy min: 0.23 / SU ML: 0.2 / σ(F): 0 / Phase error: 18.71 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.2002 2352 9.91 %random
Rwork0.1689 ---
obs0.1721 23740 95.4 %-
all-23740 --
Solvent computationShrinkage radii: 0.72 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.573 Å2 / ksol: 0.374 e/Å3
Displacement parametersBiso max: 61.18 Å2 / Biso mean: 16.0412 Å2 / Biso min: 3.69 Å2
Baniso -1Baniso -2Baniso -3
1--1.2186 Å2-0 Å20 Å2
2---0.3607 Å2-0 Å2
3---1.5793 Å2
Refinement stepCycle: LAST / Resolution: 1.731→25.701 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1506 0 52 250 1808
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0071659
X-RAY DIFFRACTIONf_angle_d1.1212276
X-RAY DIFFRACTIONf_chiral_restr0.238276
X-RAY DIFFRACTIONf_plane_restr0.005281
X-RAY DIFFRACTIONf_dihedral_angle_d18.054641
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 (%)
1.7314-1.79330.25642260.21231953217989
1.7933-1.86510.23752330.17652073230694
1.8651-1.94990.20542150.16482095231095
1.9499-2.05270.22732260.16232098232496
2.0527-2.18120.22132250.16522149237496
2.1812-2.34960.20412290.16692147237697
2.3496-2.58580.22742620.17652169243197
2.5858-2.95950.20492420.18152213245598
2.9595-3.72680.19932310.17042247247898
3.7268-25.70380.15342630.15342244250794

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