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- PDB-2o4l: Crystal Structure of HIV-1 Protease (Q7K, I50V) in Complex with T... -

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Basic information

Entry
Database: PDB / ID: 2o4l
TitleCrystal Structure of HIV-1 Protease (Q7K, I50V) in Complex with Tipranavir
Componentsprotease
KeywordsVIRAL PROTEIN / protease
Function / homology
Function and homology information


HIV-1 retropepsin / 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 ...HIV-1 retropepsin / 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 / host cell / RNA-DNA hybrid ribonuclease activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / symbiont-mediated suppression of host gene expression / 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 / 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. / Retroviral nucleocapsid Gag protein p24, C-terminal domain / Gag protein p24 C-terminal domain / Retropepsin-like catalytic domain / Matrix protein, lentiviral and alpha-retroviral, N-terminal / Ribonuclease H domain / RNase H type-1 domain profile. / 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 / Retrovirus capsid, C-terminal / Retroviral matrix protein / Retrovirus capsid, N-terminal / zinc finger / Zinc knuckle / Cathepsin D, subunit A; domain 1 / Acid Proteases / 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. / 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
Chem-TPV / Gag-Pol polyprotein / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsArmstrong, A.A. / Muzammil, S. / Jakalian, A. / Bonneau, P.R. / Schmelmer, V. / Freire, E. / Amzel, L.M.
CitationJournal: J.Virol. / Year: 2007
Title: Unique thermodynamic response of tipranavir to human immunodeficiency virus type 1 protease drug resistance mutations.
Authors: Muzammil, S. / Armstrong, A.A. / Kang, L.W. / Jakalian, A. / Bonneau, P.R. / Schmelmer, V. / Amzel, L.M. / Freire, E.
History
DepositionDec 4, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 12, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Revision 1.4Oct 20, 2021Group: Database references / Derived calculations / Category: 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
Revision 1.5Aug 30, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)22,4397
Polymers21,5822
Non-polymers8585
Water6,846380
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-42 kcal/mol
Surface area9350 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)58.957, 86.411, 46.186
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11B-595-

HOH

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Components

#1: Protein protease


Mass: 10790.780 Da / Num. of mol.: 2 / Mutation: Q7K, I50V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Genus: Lentivirus / Strain: Subtype B / Gene: gag-pol / Plasmid: pET24 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P03367, UniProt: Q1G1C3*PLUS
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: 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


Mass: 602.664 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C31H33F3N2O5S / Comment: protease inhibitor*YM
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 380 / 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: 2.72 Å3/Da / Density % sol: 54.85 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: 0.75-1.5 M NaCl, 100 mM citrate buffer pH 5.4-6.4, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.008 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 18, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.008 Å / Relative weight: 1
ReflectionResolution: 1.33→24.35 Å / Num. obs: 46728 / % possible obs: 85 % / Redundancy: 5.8 % / Rmerge(I) obs: 0.077 / Rsym value: 0.077 / Χ2: 4.03 / Net I/σ(I): 17.5
Reflection shellResolution: 1.33→1.38 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.397 / Mean I/σ(I) obs: 5.62 / Num. unique all: 4770 / Rsym value: 0.397 / Χ2: 2.795 / % possible all: 88.5

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Phasing

Phasing MRRfactor: 0.6 / Cor.coef. Fo:Fc: 0.202
Highest resolutionLowest resolution
Rotation3.5 Å48.7 Å
Translation3.5 Å48.7 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1MSM

1msm


Resolution: 1.33→24.35 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.625 / SU ML: 0.035 / Cross valid method: THROUGHOUT / ESU R: 0.069 / ESU R Free: 0.07 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.216 4719 10.1 %RANDOM
Rwork0.19 ---
obs0.193 46642 84.99 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 16.639 Å2
Baniso -1Baniso -2Baniso -3
1--0.01 Å20 Å20 Å2
2---0.05 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.33→24.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1514 0 56 380 1950
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0221732
X-RAY DIFFRACTIONr_angle_refined_deg1.3272.0542358
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.6785207
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.992556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.93915311
X-RAY DIFFRACTIONr_dihedral_angle_4_deg7.585158
X-RAY DIFFRACTIONr_chiral_restr0.0810.2279
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021226
X-RAY DIFFRACTIONr_nbd_refined0.1850.2777
X-RAY DIFFRACTIONr_nbtor_refined0.3020.21187
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0990.2260
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1240.225
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.0820.229
X-RAY DIFFRACTIONr_mcbond_it0.7161.51076
X-RAY DIFFRACTIONr_mcangle_it1.04521688
X-RAY DIFFRACTIONr_scbond_it1.6423757
X-RAY DIFFRACTIONr_scangle_it2.3944.5670
LS refinement shellResolution: 1.331→1.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 355 -
Rwork0.259 3110 -
obs-3465 86.91 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.5295-0.09460.30670.57570.13331.04640.03430.0857-0.0278-0.0575-0.0479-0.00770.06490.13770.0137-0.02260.00760.0045-0.00120.0134-0.046-14.711.34610.149
20.17550.04420.00620.94490.31810.7944-0.0016-0.02380.01780.0543-0.00820.0229-0.00420.06010.0098-0.038-0.0055-0.0005-0.01650.0099-0.0268-12.97422.47628.584
38.61955.72271.72486.7640.58551.0357-0.0632-0.12240.0622-0.2565-0.07640.0677-0.1094-0.00490.1396-0.05660.0089-0.0001-0.04240.0063-0.073-17.26619.88217.477
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: ALL

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA1 - 991 - 99
22BB1 - 991 - 99
33AE403

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