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- PDB-4obd: Crystal Structure of Nelfinavir-Resistant, Inactive HIV-1 Proteas... -
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Open data
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Basic information
Entry | Database: PDB / ID: 4obd | ||||||
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Title | Crystal Structure of Nelfinavir-Resistant, Inactive HIV-1 Protease (D30N/N88D) in Complex with the p1-p6 substrate variant (L449F/S451N) | ||||||
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Function / homology | ![]() viral budding via host ESCRT complex / RNA stem-loop binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() ![]() | ||||||
![]() | Kolli, M. | ||||||
![]() | ![]() Title: HIV-1 protease-substrate coevolution in nelfinavir resistance. Authors: Kolli, M. / Ozen, A. / Kurt-Yilmaz, N. / Schiffer, C.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 124.1 KB | Display | ![]() |
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PDB format | ![]() | 97.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 4obfC ![]() 4obgC ![]() 4obhC ![]() 4objC ![]() 4obkC ![]() 1t3rS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 10814.804 Da / Num. of mol.: 4 / Mutation: Q7K, D25N, D30N, N88D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Protein/peptide | Mass: 1234.366 Da / Num. of mol.: 2 / Fragment: UNP residues 446-455 / Mutation: L6F, S8N / Source method: obtained synthetically / Source: (synth.) ![]() ![]() ![]() #3: Chemical | ChemComp-GOL / | ![]() #4: Chemical | ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.97 Å3/Da / Density % sol: 37.55 % |
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Crystal grow![]() | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 24% PEG 5000, 0.3M ammonium sulfate, 0.5M MES monohydrate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Mar 9, 2009 / Details: Mirrors |
Radiation | Monochromator: Si(111) double-crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.68→50 Å / Num. obs: 39171 / % possible obs: 98.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 2 / Redundancy: 3.8 % / Rsym value: 0.064 / Net I/σ(I): 16.85 |
-Phasing
Phasing![]() | Method: ![]() | |||||||||
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Phasing MR | Rfactor: 45.42 / Model details: Phaser MODE: MR_AUTO
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB entry 1T3R Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.91 / Occupancy max: 1 / Occupancy min: 0.5 / SU B: 5.129 / SU ML: 0.119 / Isotropic thermal model: Overall / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.998 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
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Refine LS restraints |
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