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- PDB-4he9: Crystal Structure of HIV-1 protease mutants I54M complexed with i... -

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Basic information

Entry
Database: PDB / ID: 4he9
TitleCrystal Structure of HIV-1 protease mutants I54M complexed with inhibitor GRL-0519
ComponentsHIV-1 protease
KeywordsHYDROLASE/Hydrolase Inhibitor / aspartic acid protease / drug resistance / HIV-1 protease inhibitor GRL-0519 / 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 / DNA integration / host multivesicular body / 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 / DNA integration / host multivesicular body / viral genome integration into host DNA / RNA-directed DNA polymerase / establishment of integrated proviral latency / RNA stem-loop binding / viral penetration into host nucleus / 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 / Retrovirus capsid, C-terminal / Reverse transcriptase domain / Reverse transcriptase (RNA-dependent DNA polymerase) / Reverse transcriptase (RT) catalytic domain profile. / 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
Chem-G52 / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.06 Å
AuthorsShen, C.H. / Zhang, H. / Weber, I.T.
CitationJournal: J.Med.Chem. / Year: 2013
Title: Novel P2 tris-tetrahydrofuran group in antiviral compound 1 (GRL-0519) fills the S2 binding pocket of selected mutants of HIV-1 protease.
Authors: Zhang, H. / Wang, Y.F. / Shen, C.H. / Agniswamy, J. / Rao, K.V. / Xu, C.X. / Ghosh, A.K. / Harrison, R.W. / Weber, I.T.
History
DepositionOct 3, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 21, 2013Provider: repository / Type: Initial release
Revision 1.1Sep 20, 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: HIV-1 protease
B: HIV-1 protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,3229
Polymers21,5172
Non-polymers8057
Water4,378243
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4810 Å2
ΔGint-83 kcal/mol
Surface area9540 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.776, 85.842, 46.017
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 HIV-1 protease / PR / Retropepsin


Mass: 10758.715 Da / Num. of mol.: 2 / Fragment: UNP residues 501-599 / Mutation: Q7K, L33I, I54M, L63I, C67A, C95A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Strain: BRU/LAI / Gene: gag-pol / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: P03367, HIV-1 retropepsin
#2: Chemical ChemComp-G52 / (3R,3aS,3bR,6aS,7aS)-octahydrodifuro[2,3-b:3',2'-d]furan-3-yl [(1S,2R)-1-benzyl-2-hydroxy-3-{[(4-methoxyphenyl)sulfonyl](2-methylpropyl)amino}propyl]carbamate


Mass: 604.712 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H40N2O9S
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 2.7 Å3/Da / Density % sol: 54.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6
Details: 0.6-0.93 M NaCl, 0.06 M Sodium Acetate, pH 4.6-5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 0.8 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Aug 15, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8 Å / Relative weight: 1
ReflectionResolution: 1.06→50 Å / Num. all: 103379 / Num. obs: 103379 / % possible obs: 97.4 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.06→1.1 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.568 / Mean I/σ(I) obs: 2.1 / % possible all: 85.6

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Processing

Software
NameClassification
HKL-2000data collection
PHASERphasing
SHELXL-97refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2F8G

2f8g


Resolution: 1.06→10 Å / Num. parameters: 18629 / Num. restraintsaints: 26129 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER / Details: ANISOTROPIC REFINEMENT REDUCED FREE R (NO CUTOFF)
RfactorNum. reflection% reflectionSelection details
Rfree0.177 5164 5 %RANDOM
obs0.15 99238 97.4 %-
Refine analyzeNum. disordered residues: 37 / Occupancy sum hydrogen: 1637.69 / Occupancy sum non hydrogen: 1788.85
Refinement stepCycle: LAST / Resolution: 1.06→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1512 0 48 243 1803
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.016
X-RAY DIFFRACTIONs_angle_d0.038
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.035
X-RAY DIFFRACTIONs_zero_chiral_vol0.099
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.092
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.037
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.05
X-RAY DIFFRACTIONs_approx_iso_adps0.098

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