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- PDB-6xd2: Porcine pepsin in complex with darunavir -

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Basic information

Entry
Database: PDB / ID: 6xd2
TitlePorcine pepsin in complex with darunavir
ComponentsPepsin A
KeywordsHYDROLASE/INHIBITOR / Pepsin / inhibitor / HIV / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


Surfactant metabolism / pepsin A / digestion / aspartic-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Pepsin catalytic domain / Aspartic peptidase, N-terminal / A1 Propeptide / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Biological speciesSus scrofa (pig)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsVuksanovic, N. / Silvaggi, N.R.
CitationJournal: To Be Published
Title: Porcine pepsin in complex with darunavir
Authors: Vuksanovic, N. / Silvaggi, N.R.
History
DepositionJun 9, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 16, 2021Provider: repository / Type: Initial release
Revision 1.1Oct 18, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Pepsin A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)35,1412
Polymers34,5931
Non-polymers5481
Water6,539363
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.245, 66.245, 290.049
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number179
Space group name H-MP6522
Space group name HallP652(x,y,z+1/12)
Components on special symmetry positions
IDModelComponents
11A-765-

HOH

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Components

#1: Protein Pepsin A


Mass: 34593.484 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Sus scrofa (pig) / References: UniProt: P00791, pepsin A
#2: Chemical ChemComp-017 / (3R,3AS,6AR)-HEXAHYDROFURO[2,3-B]FURAN-3-YL(1S,2R)-3-[[(4-AMINOPHENYL)SULFONYL](ISOBUTYL)AMINO]-1-BENZYL-2-HYDROXYPROPYLCARBAMATE / Darunavir / TMC114 / UIC-94017


Mass: 547.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H37N3O7S / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 363 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.67 Å3/Da / Density % sol: 54.01 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 3.5 M Ammonium Chloride, 0.1 M sodium acetate pH 4.6

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Nov 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.9→49.34 Å / Num. obs: 30916 / % possible obs: 99.85 % / Redundancy: 12 % / Biso Wilson estimate: 18.85 Å2 / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.08851 / Rpim(I) all: 0.02635 / Rrim(I) all: 0.09249 / Net I/σ(I): 35.71
Reflection shellResolution: 1.901→1.969 Å / Rmerge(I) obs: 0.2532 / Mean I/σ(I) obs: 10.34 / Num. unique obs: 2998 / CC1/2: 0.981 / CC star: 0.995 / Rpim(I) all: 0.07655 / Rrim(I) all: 0.2648

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Processing

Software
NameVersionClassification
PHENIX1.16_3549refinement
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4PEP

4pep


Resolution: 1.9→49.34 Å / SU ML: 0.1469 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 17.7407
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflectionSelection details
Rfree0.1976 1574 5.1 %RANDOM
Rwork0.1628 29319 --
obs0.1645 30893 99.82 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 22.61 Å2
Refinement stepCycle: LAST / Resolution: 1.9→49.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2408 0 38 363 2809
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00722503
X-RAY DIFFRACTIONf_angle_d0.89793430
X-RAY DIFFRACTIONf_chiral_restr0.059393
X-RAY DIFFRACTIONf_plane_restr0.0055443
X-RAY DIFFRACTIONf_dihedral_angle_d6.63821448
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9-1.960.19071090.16462597X-RAY DIFFRACTION99.45
1.96-2.030.21011350.15912592X-RAY DIFFRACTION99.89
2.03-2.110.17611430.16262608X-RAY DIFFRACTION99.93
2.11-2.210.2161520.15662620X-RAY DIFFRACTION99.93
2.21-2.330.19581420.15662582X-RAY DIFFRACTION99.96
2.33-2.470.22941640.16252629X-RAY DIFFRACTION100
2.47-2.660.21021260.16562657X-RAY DIFFRACTION99.96
2.66-2.930.20121540.17262643X-RAY DIFFRACTION100
2.93-3.350.20691490.1712699X-RAY DIFFRACTION99.89
3.35-4.230.19121350.1492748X-RAY DIFFRACTION99.76
4.23-49.340.17781650.16882944X-RAY DIFFRACTION99.33

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