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Yorodumi- PDB-4kb9: Crystal structure of wild-type HIV-1 protease with novel tricycli... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4kb9 | ||||||
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Title | Crystal structure of wild-type HIV-1 protease with novel tricyclic P2-ligands GRL-0739A | ||||||
Components | Protease | ||||||
Keywords | Hydrolase/Hydrolase Inhibitor / spartic acid protease / HIV-1 protease inhibitor GRL-0739A / a Novel Tricyclic P2-ligand / Hydrolase-Hydrolase Inhibitor complex | ||||||
Function / homology | Function and homology information aspartic-type endopeptidase activity / proteolysis / identical protein binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.29 Å | ||||||
Authors | Wang, Y.-F. / Agniswamy, J. / Weber, I.T. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Highly Potent HIV-1 Protease Inhibitors with Novel Tricyclic P2 Ligands: Design, Synthesis, and Protein-Ligand X-ray Studies. Authors: Ghosh, A.K. / Parham, G.L. / Martyr, C.D. / Nyalapatla, P.R. / Osswald, H.L. / Agniswamy, J. / Wang, Y.F. / Amano, M. / Weber, I.T. / Mitsuya, H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4kb9.cif.gz | 111.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4kb9.ent.gz | 84.7 KB | Display | PDB format |
PDBx/mmJSON format | 4kb9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4kb9_validation.pdf.gz | 1012.6 KB | Display | wwPDB validaton report |
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Full document | 4kb9_full_validation.pdf.gz | 1018.1 KB | Display | |
Data in XML | 4kb9_validation.xml.gz | 14.1 KB | Display | |
Data in CIF | 4kb9_validation.cif.gz | 19.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kb/4kb9 ftp://data.pdbj.org/pub/pdb/validation_reports/kb/4kb9 | HTTPS FTP |
-Related structure data
Related structure data | 3nu3S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 10740.677 Da / Num. of mol.: 2 / Mutation: Q7K, L33I, L63I, C67A, C95A Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Gene: pol / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Bl21(de3) / References: UniProt: Q7SSI0, HIV-1 retropepsin |
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-Non-polymers , 6 types, 229 molecules
#2: Chemical | ChemComp-G79 / ( | ||||||||
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#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-NA / | #6: Chemical | #7: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 54.52 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 1.15 M NaCl + 0.1 M Na acetate, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 1 |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 31, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.29→50 Å / Num. all: 56283 / Num. obs: 56283 / % possible obs: 92.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 13.2 Å2 / Rmerge(I) obs: 0.061 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 1.29→1.34 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.436 / Mean I/σ(I) obs: 2 / Num. unique all: 3275 / % possible all: 54.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3NU3 Resolution: 1.29→10 Å / Num. parameters: 17749 / Num. restraintsaints: 23884 / Cross valid method: FREE R / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: CONJUGAGE GRADIENT MINIMIZATION
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Refine analyze | Num. disordered residues: 25 / Occupancy sum hydrogen: 1645 / Occupancy sum non hydrogen: 1741.25 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.29→10 Å
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Refine LS restraints |
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