+Open data
-Basic information
Entry | Database: PDB / ID: 8aww | ||||||
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Title | Transthyretin conjugated with a tafamidis derivative | ||||||
Components | Transthyretin | ||||||
Keywords | TRANSPORT PROTEIN / TTR / tafamidis / protein-drug conjugates / drug design / cancer therapy. | ||||||
Function / homology | Function and homology information Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation ...Retinoid cycle disease events / thyroid hormone binding / The canonical retinoid cycle in rods (twilight vision) / Non-integrin membrane-ECM interactions / purine nucleobase metabolic process / Retinoid metabolism and transport / hormone activity / azurophil granule lumen / Amyloid fiber formation / Neutrophil degranulation / extracellular space / extracellular exosome / extracellular region / identical protein binding Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Cerofolini, L. / Vasa, K. / Bianconi, E. / Salobehaj, M. / Cappelli, G. / Licciardi, G. / Perez-Rafols, A. / Padilla Cortes, L.D. / Antonacci, S. / Rizzo, D. ...Cerofolini, L. / Vasa, K. / Bianconi, E. / Salobehaj, M. / Cappelli, G. / Licciardi, G. / Perez-Rafols, A. / Padilla Cortes, L.D. / Antonacci, S. / Rizzo, D. / Ravera, E. / Calderone, V. / Parigi, G. / Luchinat, C. / Macchiarulo, A. / Menichetti, S. / Fragai, M. | ||||||
Funding support | European Union, 1items
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Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2023 Title: Combining Solid-State NMR with Structural and Biophysical Techniques to Design Challenging Protein-Drug Conjugates. Authors: Cerofolini, L. / Vasa, K. / Bianconi, E. / Salobehaj, M. / Cappelli, G. / Bonciani, A. / Licciardi, G. / Perez-Rafols, A. / Padilla-Cortes, L. / Antonacci, S. / Rizzo, D. / Ravera, E. / ...Authors: Cerofolini, L. / Vasa, K. / Bianconi, E. / Salobehaj, M. / Cappelli, G. / Bonciani, A. / Licciardi, G. / Perez-Rafols, A. / Padilla-Cortes, L. / Antonacci, S. / Rizzo, D. / Ravera, E. / Viglianisi, C. / Calderone, V. / Parigi, G. / Luchinat, C. / Macchiarulo, A. / Menichetti, S. / Fragai, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8aww.cif.gz | 65.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8aww.ent.gz | 46.8 KB | Display | PDB format |
PDBx/mmJSON format | 8aww.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/aw/8aww ftp://data.pdbj.org/pub/pdb/validation_reports/aw/8aww | HTTPS FTP |
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-Related structure data
Related structure data | 3tctS S: Starting model for refinement |
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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 on special symmetry positions |
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-Components
#1: Protein | Mass: 12703.217 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TTR, PALB / Production host: Escherichia coli (E. coli) / References: UniProt: P02766 #2: Chemical | #3: 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: 2.34 Å3/Da / Density % sol: 47.39 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.5 / Details: 1.4 M sodium citrate |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: BRUKER D8 QUEST / Wavelength: 1.541 Å |
Detector | Type: Bruker PHOTON III / Detector: PIXEL / Date: Nov 3, 2021 / Details: mirrors |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.541 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→35.47 Å / Num. obs: 31504 / % possible obs: 98.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 12.2 % / CC1/2: 1 / Rmerge(I) obs: 0.08 / Net I/σ(I): 22.2 |
Reflection shell | Resolution: 1.6→1.657 Å / Rmerge(I) obs: 0.9 / Mean I/σ(I) obs: 2 / Num. unique obs: 2783 / CC1/2: 0.67 / % possible all: 88.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3tct Resolution: 1.6→35.47 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.45 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 94.71 Å2 / Biso mean: 23.7774 Å2 / Biso min: 9.89 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.6→35.47 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 11
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