+Open data
-Basic information
Entry | Database: PDB / ID: 4yhk | ||||||
---|---|---|---|---|---|---|---|
Title | Reversal Agent for Dabigatran | ||||||
Components |
| ||||||
Keywords | IMMUNE SYSTEM / Antibody / Dabigatran / Pradaxa / Antidote / Reversal Agent | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-4CC Function and homology information | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.21 Å | ||||||
Authors | Schiele, F. / Nar, H. | ||||||
Citation | Journal: Mabs / Year: 2015 Title: Structure-guided residence time optimization of a dabigatran reversal agent. Authors: Schiele, F. / van Ryn, J. / Litzenburger, T. / Ritter, M. / Seeliger, D. / Nar, H. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4yhk.cif.gz | 104.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4yhk.ent.gz | 78.2 KB | Display | PDB format |
PDBx/mmJSON format | 4yhk.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yh/4yhk ftp://data.pdbj.org/pub/pdb/validation_reports/yh/4yhk | HTTPS FTP |
---|
-Related structure data
Related structure data | 4ygvC 4yhiC 4yhlC 4yhmC 4yhnC 4yhoC 1c1eS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
#1: Antibody | Mass: 23744.479 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetinae (hamsters) | ||
---|---|---|---|
#2: Antibody | Mass: 24116.936 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetinae (hamsters) | ||
#3: Chemical | ChemComp-4CC / | ||
#4: Chemical | #5: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
---|
-Sample preparation
Crystal | Density Matthews: 1.92 Å3/Da / Density % sol: 35.96 % |
---|---|
Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM SPG buffer (pH 6) and 25% PEG 1500 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91 Å |
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91 Å / Relative weight: 1 |
Reflection | Resolution: 2.21→127.69 Å / Num. obs: 19263 / % possible obs: 99.9 % / Redundancy: 6.2 % / Biso Wilson estimate: 31.5 Å2 / Rmerge(I) obs: 0.15 / Net I/σ(I): 9.8 |
Reflection shell | Resolution: 2.21→2.33 Å / Redundancy: 6.2 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3.2 / % possible all: 99.8 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1C1E Resolution: 2.21→40 Å / Cor.coef. Fo:Fc: 0.9235 / Cor.coef. Fo:Fc free: 0.8858 / SU R Cruickshank DPI: 0.347 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.42 / SU Rfree Blow DPI: 0.231 / SU Rfree Cruickshank DPI: 0.226
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 28.64 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.224 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: 1 / Resolution: 2.21→40 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.21→2.33 Å / Total num. of bins used: 10
|