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- PDB-7dt9: D30N HIV Protease in complex with Saquinavir -

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Basic information

Entry
Database: PDB / ID: 7dt9
TitleD30N HIV Protease in complex with Saquinavir
ComponentsProtease
KeywordsVIRAL PROTEIN / HIV Protease / Drug resistance / AIDS
Function / homology
Function and homology information


aspartic-type endopeptidase activity / proteolysis
Similarity search - Function
Retropepsin-like catalytic domain / Retropepsins / Retroviral aspartyl protease / Aspartyl protease, retroviral-type family profile. / Peptidase A2A, retrovirus, catalytic / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
Saquinavir / Chem-ROC / Pol polyprotein
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsBihani, S.C. / Hosur, M.V.
CitationJournal: To Be Published
Title: D30N HIV Protease in complex with Saquinavir
Authors: Bihani, S.C. / Hosur, M.V.
History
DepositionJan 4, 2021Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jan 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 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
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,6042
Polymers21,9331
Non-polymers6711
Water1,856103
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1240 Å2
ΔGint-2 kcal/mol
Surface area9610 Å2
MethodPISA
Unit cell
Length a, b, c (Å)62.730, 62.730, 82.330
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number169
Space group name H-MP61
Space group name HallP61
Symmetry operation#1: x,y,z
#2: x-y,x,z+1/6
#3: y,-x+y,z+5/6
#4: -y,x-y,z+1/3
#5: -x+y,-x,z+2/3
#6: -x,-y,z+1/2

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Components

#1: Protein Protease / Retropepsin


Mass: 21932.789 Da / Num. of mol.: 1 / Mutation: D30N,C95M,D1030N,C1095A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Production host: Escherichia coli (E. coli) / References: UniProt: Q72874
#2: 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


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


Mass: 18.015 Da / Num. of mol.: 103 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.13 Å3/Da / Density % sol: 42.31 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: NaCl (1.5M), Sodium acetate buffer (50 mM, pH 4.5)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM30A / Wavelength: 0.934 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 6, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 1.89→32.81 Å / Num. obs: 14267 / % possible obs: 96.6 % / Redundancy: 5.7 % / Biso Wilson estimate: 26.28 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 21.43
Reflection shellResolution: 1.89→1.99 Å / Rmerge(I) obs: 0.685 / Num. unique obs: 1919

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Processing

Software
NameVersionClassification
PHENIX1.18.2_3874refinement
XDSdata reduction
XSCALEdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7DPQ

7dpq


Resolution: 1.89→32.81 Å / SU ML: 0.2181 / Cross valid method: FREE R-VALUE / σ(F): 1.37 / Phase error: 23.8359
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2093 714 5.01 %
Rwork0.1747 13551 -
obs0.1764 14265 97.22 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 34.95 Å2
Refinement stepCycle: LAST / Resolution: 1.89→32.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1516 0 49 103 1668
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00641648
X-RAY DIFFRACTIONf_angle_d0.94592239
X-RAY DIFFRACTIONf_chiral_restr0.0569262
X-RAY DIFFRACTIONf_plane_restr0.0053273
X-RAY DIFFRACTIONf_dihedral_angle_d19.0861600
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.89-2.040.2891400.22492659X-RAY DIFFRACTION95.95
2.04-2.240.2471420.20142693X-RAY DIFFRACTION97.06
2.24-2.570.22291430.18042710X-RAY DIFFRACTION97.41
2.57-3.240.241430.18282730X-RAY DIFFRACTION98.05
3.24-32.810.16891460.15422759X-RAY DIFFRACTION97.68
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)
15.045803779242.005848462342.673940562422.673102144170.9626068961733.91174500617-0.05977895928610.39902310872-0.323461708491-0.2242700089530.192673314384-0.1264726336350.04001605727430.226112012518-0.08032645688470.162666752474-0.0431930452041-0.001790165643090.212243337391-0.01218116927370.190337065162-17.333768491716.6571610919.3688337111
24.582695952642.143673059871.823151561353.452947896151.774087248793.073005623390.183350036412-0.278780676628-0.2425479910140.280822443531-0.0415217137895-0.2906706146070.210504522746-0.139343691847-0.1046819034570.168334275933-0.0455176714107-0.002450098799210.2153036963080.008569171957380.186724479012-5.7864887556623.332363329136.8018326451
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 1 through 99 )1 - 991 - 99
22chain 'A' and (resid 1001 through 1099 )1001 - 1099100 - 198

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