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- PDB-3ogp: Crystal Structure of 6s-98S FIV Protease with Darunavir bound -

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Basic information

Entry
Database: PDB / ID: 3ogp
TitleCrystal Structure of 6s-98S FIV Protease with Darunavir bound
ComponentsFIV Protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / aspartyl protease / HIV-like FIV chimera / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / retroviral ribonuclease H / exoribonuclease H / exoribonuclease H activity / DNA integration / viral genome integration into host DNA ...dUTP catabolic process / dUMP biosynthetic process / dUTP diphosphatase / dUTP diphosphatase activity / Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / 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-directed DNA polymerase activity / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / DNA recombination / Hydrolases; Acting on ester bonds / aspartic-type endopeptidase activity / symbiont entry into host cell / magnesium ion binding / proteolysis / DNA binding / zinc ion binding
Similarity search - Function
Deoxyuridine triphosphate nucleotidohydrolase / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb domain / Zinc finger integrase-type profile. ...Deoxyuridine triphosphate nucleotidohydrolase / dUTPase-like / dUTPase / dUTPase, trimeric / dUTPase-like superfamily / Reverse transcriptase connection / Reverse transcriptase connection domain / Reverse transcriptase thumb / Reverse transcriptase thumb 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. / 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 / 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 / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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
Chem-017 / Pol polyprotein
Similarity search - Component
Biological speciesFeline immunodeficiency virus
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsLin, Y.-C. / Perryman, A.L. / Elder, J.H. / Stout, C.D.
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: Structural basis for drug and substrate specificity exhibited by FIV encoding a chimeric FIV/HIV protease.
Authors: Lin, Y.C. / Perryman, A.L. / Olson, A.J. / Torbett, B.E. / Elder, J.H. / Stout, C.D.
History
DepositionAug 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 28, 2012Group: Database references
Revision 1.3Sep 6, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: FIV Protease
B: FIV Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6305
Polymers26,4572
Non-polymers1,1733
Water2,846158
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5810 Å2
ΔGint-37 kcal/mol
Surface area10690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)81.170, 81.170, 33.590
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31

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Components

#1: Protein FIV Protease / Protease / Retropepsin


Mass: 13228.286 Da / Num. of mol.: 2 / Fragment: UNP residues 39-154 / Mutation: I37V, N55M, V59I, I98S, Q99V, P100N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Feline immunodeficiency virus / Gene: pol, PR / Plasmid: PET-21A(+) / Production host: Escherichia coli (E. coli) / Strain (production host): ROSETTA(DE3)PLYSS
References: UniProt: P16088, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
#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.: 2 / Source method: obtained synthetically / Formula: C27H37N3O7S / Comment: medication, antiretroviral*YM
#3: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 158 / 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: 2.41 Å3/Da / Density % sol: 49.06 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL11-1 / Wavelength: 0.97945 Å
DetectorType: MARmosaic325 / Detector: CCD / Date: Jan 22, 2010 / Details: Rh coated flat mirror
RadiationMonochromator: Side scattering bent cube-root I-beam single crystal
Protocol: SINGLE WAVELENGTH / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97945 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.5
11h,-h-k,-l20.5
ReflectionResolution: 1.7→27 Å / Num. all: 27120 / Num. obs: 27120 / % possible obs: 99.5 % / Redundancy: 2.8 % / Biso Wilson estimate: 21.7 Å2 / Rsym value: 0.051 / Net I/σ(I): 12.8
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRsym value% possible all
1.7-1.792.70.3462.21042138410.34697.1
1.79-1.92.80.2083.61068238050.208100
1.9-2.032.80.1314.81003835370.131100
2.03-2.192.90.0867.7951033280.086100
2.19-2.42.80.06311.2850129970.063100
2.4-2.692.90.04914.1787227130.049100
2.69-3.12.80.0415.6692624320.04100
3.1-3.82.90.03516600820450.035100
3.8-5.382.90.04114.5452115760.041100
5.38-26.5692.90.03716.624658460.03798

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.15data scaling
REFMACrefinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2HAH

2hah


Resolution: 1.7→27 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.932 / WRfactor Rfree: 0.2324 / WRfactor Rwork: 0.1895 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8468 / SU B: 3.479 / SU ML: 0.097 / SU R Cruickshank DPI: 0.023 / SU Rfree: 0.0235 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.023 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2286 1358 5 %RANDOM
Rwork0.1852 ---
obs0.1873 25748 99.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 48.7 Å2 / Biso mean: 24.0154 Å2 / Biso min: 8.05 Å2
Baniso -1Baniso -2Baniso -3
1-5.75 Å20 Å20 Å2
2--5.75 Å20 Å2
3----11.5 Å2
Refinement stepCycle: LAST / Resolution: 1.7→27 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1778 0 80 158 2016
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0212105
X-RAY DIFFRACTIONr_angle_refined_deg1.2851.9713207
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.9237.5444
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.78924.31888
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.64615344
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0761516
X-RAY DIFFRACTIONr_chiral_restr0.120.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022272
X-RAY DIFFRACTIONr_mcbond_it0.6371.51101
X-RAY DIFFRACTIONr_mcangle_it1.11621788
X-RAY DIFFRACTIONr_scbond_it1.4963782
X-RAY DIFFRACTIONr_scangle_it2.2264.5749
LS refinement shellResolution: 1.7→1.744 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.269 100 -
Rwork0.237 1798 -
all-1898 -
obs--94.29 %

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