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- PDB-3kdc: Crystal Structure of HIV-1 Protease (Q7K, L33I, L63I) in Complex ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3kdc | ||||||
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Title | Crystal Structure of HIV-1 Protease (Q7K, L33I, L63I) in Complex with KNI-10074 | ||||||
![]() | Protease![]() | ||||||
![]() | HYDROLASE/HYDROLASE INHIBITOR / ![]() ![]() ![]() | ||||||
Function / homology | ![]() RNA stem-loop binding / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Chufan, E.E. / Kawasaki, Y. / Freire, E. / Amzel, L.M. | ||||||
![]() | ![]() Title: How much binding affinity can be gained by filling a cavity? Authors: Kawasaki, Y. / Chufan, E.E. / Lafont, V. / Hidaka, K. / Kiso, Y. / Mario Amzel, L. / Freire, E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 61.7 KB | Display | ![]() |
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PDB format | ![]() | 45 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3kdbC ![]() 3kddC ![]() 1msmS 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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Unit cell |
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Components
#1: Protein | ![]() Mass: 10804.808 Da / Num. of mol.: 2 / Fragment: UNP residues 501-599 / Mutation: Q7K, L33I, L63I Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() ![]() ![]() #2: Chemical | ChemComp-JZP / ( | #3: Chemical | ChemComp-GOL / | ![]() #4: Chemical | ChemComp-CL / ![]() #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.33 % |
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Crystal grow![]() | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: citrate buffer pH 7.2, 100 mM DTT, 3mM NaN3 and 750 mM NaCl, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jul 16, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.2→48.3 Å / Num. obs: 12408 / % possible obs: 99.8 % / Redundancy: 4.4 % / Rsym value: 0.12 / Net I/σ(I): 11.2 |
Reflection shell | Resolution: 2.2→2.28 Å / Redundancy: 4.4 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 1212 / Rsym value: 0.46 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 1MSM Resolution: 2.2→48.28 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.914 / SU B: 9.642 / SU ML: 0.141 / Cross valid method: THROUGHOUT / ESU R: 0.286 / ESU R Free: 0.218 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.917 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→48.28 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
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