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- PDB-3spk: Tipranavir in Complex with a Human Immunodeficiency Virus Type 1 ... -

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Basic information

Entry
Database: PDB / ID: 3spk
TitleTipranavir in Complex with a Human Immunodeficiency Virus Type 1 Protease Variant
ComponentsHIV-1 protease
KeywordsHYDORLASE/HYDORLASE INHIBITOR / tipranavir / multi-drug resistant HIV-1 protease / HYDORLASE-HYDORLASE INHIBITOR complex
Function / homology
Function and homology information


viral genome integration into host DNA / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / endonuclease activity / aspartic-type endopeptidase activity / proteolysis / DNA binding
Similarity search - Function
Reverse transcriptase thumb / Reverse transcriptase thumb domain / Retropepsin-like catalytic domain / Reverse transcriptase (RNA-dependent DNA polymerase) / 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 thumb / Reverse transcriptase thumb domain / Retropepsin-like catalytic domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase domain / 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 / Reverse transcriptase/Diguanylate cyclase domain / DNA/RNA polymerase superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
Chem-TPV / Pol protein
Similarity search - Component
Biological specieshuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.24 Å
AuthorsWang, Y. / Liu, Z. / Brunzelle, J.S. / Kovari, I.A. / Kovari, L.C.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: The higher barrier of darunavir and tipranavir resistance for HIV-1 protease.
Authors: Wang, Y. / Liu, Z. / Brunzelle, J.S. / Kovari, I.A. / Dewdney, T.G. / Reiter, S.J. / Kovari, L.C.
History
DepositionJul 1, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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
Remark 999Author states that they are characteristic mutations of the original patient isolate MDR769 HIV-1 protease.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: HIV-1 protease
B: HIV-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,7474
Polymers21,5412
Non-polymers1,2052
Water6,323351
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6090 Å2
ΔGint-25 kcal/mol
Surface area9320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.119, 63.119, 83.540
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Protein HIV-1 protease /


Mass: 10770.686 Da / Num. of mol.: 2 / Fragment: HIV-1 protease
Mutation: Q7K, L10I, M36V, M46L, I54V, I62V, L63P, A71V, V82T, I84V, L90M
Source method: isolated from a genetically manipulated source
Details: The sequence is a clinical isolate with mutations introduced.
Source: (gene. exp.) human immunodeficiency virus type 1 / Gene: pol / Plasmid: pET21b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q000H7, HIV-1 retropepsin
#2: Chemical ChemComp-TPV / N-(3-{(1R)-1-[(6R)-4-HYDROXY-2-OXO-6-PHENETHYL-6-PROPYL-5,6-DIHYDRO-2H-PYRAN-3-YL]PROPYL}PHENYL)-5-(TRIFLUOROMETHYL)-2-PYRIDINESULFONAMIDE / TIPRANAVIR / Tipranavir


Mass: 602.664 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C31H33F3N2O5S / Comment: protease inhibitor*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 351 / 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: 2.23 Å3/Da / Density % sol: 44.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 6
Details: 0.1M MES and 2.4M ammonium sulfate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 0.979 Å
DetectorType: RAYONIX MX-225 / Detector: CCD / Date: Nov 18, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.2→29.523 Å / Num. all: 51650 / Num. obs: 51613 / % possible obs: 99.9 % / Redundancy: 9.1 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 3.43

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Processing

Software
NameVersionClassification
HKL-2000data collection
AMoREphasing
REFMAC5.5.0102refinement
DENZOdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.24→29.523 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.22702 2573 Random
Rwork0.17396 --
obs0.17658 51613 -
all-51650 -
Displacement parametersBiso mean: 17.293 Å2
Baniso -1Baniso -2Baniso -3
1-0.22 Å20.11 Å20 Å2
2--0.22 Å20 Å2
3----0.33 Å2
Refinement stepCycle: LAST / Resolution: 1.24→29.523 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 84 351 1949
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_refined_d0.01
X-RAY DIFFRACTIONr_angle_refined_deg1.368
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.193
X-RAY DIFFRACTIONr_dihedral_angle_2_deg45.53
X-RAY DIFFRACTIONr_chiral_restr0.333
X-RAY DIFFRACTIONr_gen_planes_refined0.018
X-RAY DIFFRACTIONr_mcbond_it3.362
X-RAY DIFFRACTIONr_mcangle_it4.797
X-RAY DIFFRACTIONr_scbond_it6.261
X-RAY DIFFRACTIONr_scangle_it8.394
X-RAY DIFFRACTIONr_rigid_bond_restr3.466

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