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- PDB-3d1y: Crystal structure of HIV-1 mutant I54V and inhibitor SAQUINA -

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Basic information

Entry
Database: PDB / ID: 3d1y
TitleCrystal structure of HIV-1 mutant I54V and inhibitor SAQUINA
ComponentsHIV-1 Protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / DRUG RESISTANCE / HIV-1 / I54V / flap mutant / AIDS / Aspartyl protease / Capsid maturation / Capsid protein / Protease / hydrolase-hydrolase inhibitor complex
Function / homology
Function and homology information


HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA ...HIV-1 retropepsin / : / retroviral ribonuclease H / exoribonuclease H / : / exoribonuclease H activity / host multivesicular body / DNA integration / RNA-directed DNA polymerase / viral genome integration into host DNA / viral penetration into host nucleus / establishment of integrated proviral latency / RNA-directed DNA polymerase activity / Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases / RNA-DNA hybrid ribonuclease activity / viral nucleocapsid / DNA recombination / Hydrolases; Acting on ester bonds / DNA-directed DNA polymerase / aspartic-type endopeptidase activity / DNA-directed DNA polymerase activity / symbiont entry into host cell / symbiont-mediated suppression of host gene expression / lipid binding / host cell nucleus / host cell plasma membrane / virion membrane / structural molecule activity / proteolysis / DNA binding / RNA 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 / Zinc finger, CCHC-type superfamily / Cathepsin D, subunit A; domain 1 / Acid Proteases / Zinc finger, CCHC-type / Zinc finger CCHC-type profile. / Ribonuclease H superfamily / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / 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
Saquinavir / Chem-ROC / Gag-Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus type 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / AB INITIO / Resolution: 1.05 Å
AuthorsLiu, F. / Weber, I.T.
Citation
Journal: J.Mol.Biol. / Year: 2008
Title: Effect of flap mutations on structure of HIV-1 protease and inhibition by saquinavir and darunavir.
Authors: Liu, F. / Kovalevsky, A.Y. / Tie, Y. / Ghosh, A.K. / Harrison, R.W. / Weber, I.T.
#1: Journal: J.Mol.Biol. / Year: 2006
Title: Ultra-High Resolution Crystal Structure of HIV-1 Protease Mutant Reveals Two Binding Sites for Clinical Inhibitor Tmc114
Authors: Kovalevsky, A.Y. / Liu, F. / Leshchenko, S. / Ghosh, A.K. / Harrison, R.W. / Weber, I.T.
#2: Journal: J.Mol.Biol. / Year: 2005
Title: Kinetic, Stability, and Structural Changes in High-Resolution Crystal Structures of HIV-1 Protease with Drug-Resistant Mutations L24I, I50V, and G73S.
Authors: Liu, F. / Boross, P.I. / Wang, Y.F. / Tozser, J. / Louis, J.M. / Harrison, R.W. / Weber, I.T.
History
DepositionMay 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 27, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / Version format compliance
Revision 1.2Feb 27, 2013Group: Other
Revision 1.3Oct 20, 2021Group: Database references / Derived calculations / Structure summary
Category: chem_comp / database_2 ...chem_comp / database_2 / entity / pdbx_entity_nonpoly / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 21, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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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)22,2186
Polymers21,4532
Non-polymers7654
Water4,017223
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5470 Å2
ΔGint-52 kcal/mol
Surface area9600 Å2
MethodPISA
Unit cell
Length a, b, c (Å)58.720, 85.940, 46.380
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 / / Retropepsin / PR


Mass: 10726.649 Da / Num. of mol.: 2 / Mutation: I54V
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus type 1 / Gene: gag-pol / Production host: Escherichia coli (E. coli) / References: UniProt: P04587, HIV-1 retropepsin
#2: Chemical ChemComp-NA / SODIUM ION


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


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ROC / (2S)-N-[(2S,3R)-4-[(2S,3S,4aS,8aS)-3-(tert-butylcarbamoyl)-3,4,4a,5,6,7,8,8a-octahydro-1H-isoquinolin-2-yl]-3-hydroxy-1 -phenyl-butan-2-yl]-2-(quinolin-2-ylcarbonylamino)butanediamide / / Fortovase / SAQUINAVIR / RO 31-8959 / Saquinavir


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 670.841 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C38H50N6O5 / References: Saquinavir / Comment: medication, antiretroviral*YM
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 223 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsTHE INHIBITOR ROC IS A HYDROXYETHYLAMINE CONTAINING TRANSITION STATE MIMETIC.
Sequence detailsMUTATIONS Q7K, L33I, L63I, C67A, C95A, HAVE BEEN MADE TO STABILIZE THE PROTEASE FROM ...MUTATIONS Q7K, L33I, L63I, C67A, C95A, HAVE BEEN MADE TO STABILIZE THE PROTEASE FROM AUTOPROTEOLYSIS, WHILE RETAINING ACTIVITY SIMILAR TO WILD-TYPE HIV-1 PROTEASE

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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: 2.73 Å3/Da / Density % sol: 54.9 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 5.4
Details: SODIUM ACETATE BUFFER, 1M NaCl, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 95 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jun 13, 2007
RadiationMonochromator: SI / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.05→50 Å / Num. all: 101144 / Num. obs: 83460 / % possible obs: 82.5 % / Observed criterion σ(F): 4 / Observed criterion σ(I): 2 / Redundancy: 8.3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 16.8
Reflection shellResolution: 1.05→1.09 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 2.5 / % possible all: 92.5

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Processing

Software
NameClassification
SHELXmodel building
SHELXL-97refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: AB INITIO / Resolution: 1.05→10 Å / Num. parameters: 16779 / Num. restraintsaints: 21249 / 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
Rfree0.1736 5052 5 %RANDOM
Rwork0.15 ---
all-101144 --
obs-83460 82.5 %-
Refine analyzeNum. disordered residues: 17 / Occupancy sum hydrogen: 1614 / Occupancy sum non hydrogen: 1782
Refinement stepCycle: LAST / Resolution: 1.05→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1510 0 52 223 1785
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.017
X-RAY DIFFRACTIONs_angle_d0.033
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0286
X-RAY DIFFRACTIONs_zero_chiral_vol0.085
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.096
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.084
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.006
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.056
X-RAY DIFFRACTIONs_approx_iso_adps0.09

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