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Yorodumi- PDB-7wbs: Crystal structure of HIV-1 protease in complex with lactam deriva... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7wbs | ||||||
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Title | Crystal structure of HIV-1 protease in complex with lactam derivative 2 | ||||||
Components | Protease | ||||||
Keywords | HYDROLASE/INHIBITOR / HYDROLASE-Inhibitor complex | ||||||
Function / homology | Function and homology information viral genome integration into host DNA / establishment of integrated proviral latency / RNA stem-loop binding / RNA-directed DNA polymerase activity / endonuclease activity / aspartic-type endopeptidase activity / proteolysis / DNA binding Similarity search - Function | ||||||
Biological species | Human immunodeficiency virus 1 | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.85 Å | ||||||
Authors | Kojima, E. / Iimuro, A. / Nakajima, M. / Kinuta, H. / Asada, N. / Sako, Y. / Nakata, Z. / Uemura, K. / Arita, S. / Miki, S. ...Kojima, E. / Iimuro, A. / Nakajima, M. / Kinuta, H. / Asada, N. / Sako, Y. / Nakata, Z. / Uemura, K. / Arita, S. / Miki, S. / Wakabayashi-Morimoto, C. / Tachibana, Y. / Fumoto, M. | ||||||
Funding support | 1items
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Citation | Journal: J.Med.Chem. / Year: 2022 Title: Pocket-to-Lead: Structure-Based De Novo Design of Novel Non-peptidic HIV-1 Protease Inhibitors Using the Ligand Binding Pocket as a Template. Authors: Kojima, E. / Iimuro, A. / Nakajima, M. / Kinuta, H. / Asada, N. / Sako, Y. / Nakata, Z. / Uemura, K. / Arita, S. / Miki, S. / Wakasa-Morimoto, C. / Tachibana, Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7wbs.cif.gz | 57.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7wbs.ent.gz | 38.6 KB | Display | PDB format |
PDBx/mmJSON format | 7wbs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wb/7wbs ftp://data.pdbj.org/pub/pdb/validation_reports/wb/7wbs | HTTPS FTP |
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-Related structure data
Related structure data | 7wcqC 4ll3S S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 10830.781 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Human immunodeficiency virus 1 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WFL7 #2: Chemical | #3: Chemical | ChemComp-8LT / ( | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.69 Å3/Da / Density % sol: 54.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop Details: 0.5 M sodium chloride, 0.1 M sodium citrate tribasic dihydrate pH 5.6 and 2% v/v ethylene imine polymer |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ SUPERBRIGHT / Wavelength: 1.54178 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS VII / Detector: IMAGE PLATE / Date: Oct 18, 2019 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.85→50 Å / Num. obs: 20529 / % possible obs: 100 % / Redundancy: 6.5 % / Rmerge(I) obs: 0.033 / Rpim(I) all: 0.014 / Rrim(I) all: 0.036 / Χ2: 1.054 / Net I/σ(I): 16.3 / Num. measured all: 133470 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | ||||||
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Phasing MR | R rigid body: 0.531
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LL3 Resolution: 1.85→48.22 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.949 / SU B: 2.27 / SU ML: 0.07 / SU R Cruickshank DPI: 0.1263 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.126 / ESU R Free: 0.111 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 51.09 Å2 / Biso mean: 17.914 Å2 / Biso min: 10.74 Å2
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Refinement step | Cycle: final / Resolution: 1.85→48.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.85→1.898 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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