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- PDB-4njv: Crystal structure of multidrug-resistant clinical isolate A02 HIV... -

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Basic information

Entry
Database: PDB / ID: 4njv
TitleCrystal structure of multidrug-resistant clinical isolate A02 HIV-1 protease in complex with ritonavir
ComponentsProtease
KeywordsHydrolase/Hydrolase inhibitor / multidrug-resistance / HIV-1 protease / ritonavir / RIT / protease inhibitor / kaletra / Hydrolase-Hydrolase inhibitor complex
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 / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Retropepsin-like catalytic domain / 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 / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
RITONAVIR / RITONAVIR / Protease
Similarity search - Component
Biological speciesHuman immunodeficiency virus 1
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsYedidi, R.S. / Garimella, H. / Chang, S.B. / Kaufman, J.D. / Das, D. / Wingfield, P.T. / Mitsuya, H.
CitationJournal: Antimicrob.Agents Chemother. / Year: 2014
Title: A Conserved Hydrogen-Bonding Network of P2 bis-Tetrahydrofuran-Containing HIV-1 Protease Inhibitors (PIs) with a Protease Active-Site Amino Acid Backbone Aids in Their Activity against PI-Resistant HIV.
Authors: Yedidi, R.S. / Garimella, H. / Aoki, M. / Aoki-Ogata, H. / Desai, D.V. / Chang, S.B. / Davis, D.A. / Fyvie, W.S. / Kaufman, J.D. / Smith, D.W. / Das, D. / Wingfield, P.T. / Maeda, K. / Ghosh, A.K. / Mitsuya, H.
History
DepositionNov 11, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 2, 2014Provider: repository / Type: Initial release
Revision 1.1May 21, 2014Group: Database references
Revision 1.2Jun 25, 2014Group: Database references
Revision 1.3Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Protease
B: Protease
C: Protease
D: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)45,0736
Polymers43,6314
Non-polymers1,4422
Water6,467359
1
A: Protease
B: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5373
Polymers21,8162
Non-polymers7211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5280 Å2
ΔGint-39 kcal/mol
Surface area9410 Å2
MethodPISA
2
C: Protease
D: Protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)22,5373
Polymers21,8162
Non-polymers7211
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5300 Å2
ΔGint-39 kcal/mol
Surface area9380 Å2
MethodPISA
Unit cell
Length a, b, c (Å)45.952, 58.219, 86.866
Angle α, β, γ (deg.)90.00, 90.02, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Protease /


Mass: 10907.779 Da / Num. of mol.: 4
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: Q9J006
#2: Chemical ChemComp-RIT / RITONAVIR / / A-84538 / Ritonavir


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 720.944 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C37H48N6O5S2 / References: RITONAVIR / Comment: medication, antiretroviral*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 359 / 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: 2.66 Å3/Da / Density % sol: 53.81 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 3.0 M sodium chloride (precipitant), 0.1 M HEPES (buffer), pH 7.0, 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: 1 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Mar 13, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.8→34.813 Å / Num. obs: 40844 / Rmerge(I) obs: 0.089
Reflection shellResolution: 1.8→1.8461 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.089 / Mean I/σ(I) obs: 18.71

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Processing

Software
NameVersionClassification
HKL-2000data collection
BALBESphasing
PHENIX(phenix.refine: 1.8.1_1168)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→34.81 Å / SU ML: 0.17 / σ(F): 1.36 / Phase error: 21.62 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.216 2054 5.04 %
Rwork0.1868 --
obs0.1882 40761 96.11 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→34.81 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3064 0 100 359 3523
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093336
X-RAY DIFFRACTIONf_angle_d1.2794524
X-RAY DIFFRACTIONf_dihedral_angle_d16.5381256
X-RAY DIFFRACTIONf_chiral_restr0.086512
X-RAY DIFFRACTIONf_plane_restr0.005564
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.84610.2608960.24361737X-RAY DIFFRACTION65
1.8461-1.89230.25991270.22892259X-RAY DIFFRACTION85
1.8923-1.94340.24941390.222528X-RAY DIFFRACTION95
1.9434-2.00060.27261510.20452633X-RAY DIFFRACTION99
2.0006-2.06520.2031370.18692628X-RAY DIFFRACTION100
2.0652-2.1390.23561500.18052698X-RAY DIFFRACTION100
2.139-2.22460.20821330.17872665X-RAY DIFFRACTION100
2.2246-2.32580.23921480.19312673X-RAY DIFFRACTION100
2.3258-2.44840.23461400.20742656X-RAY DIFFRACTION100
2.4484-2.60180.26171370.21252675X-RAY DIFFRACTION100
2.6018-2.80260.24561420.21262671X-RAY DIFFRACTION100
2.8026-3.08450.23891410.20222743X-RAY DIFFRACTION100
3.0845-3.53040.18361420.18082675X-RAY DIFFRACTION100
3.5304-4.44650.1641270.14642697X-RAY DIFFRACTION100
4.4465-34.81910.19871440.17432769X-RAY DIFFRACTION99

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