+
Open data
-
Basic information
Entry | Database: PDB / ID: 5mho | |||||||||
---|---|---|---|---|---|---|---|---|---|---|
Title | FXIIIa in complex with the inhibitor ZED2369 | |||||||||
![]() |
| |||||||||
![]() | HYDROLASE / factor XIII / inhibition / transglutaminase | |||||||||
Function / homology | ![]() protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / transferase complex / peptide cross-linking / blood coagulation, fibrin clot formation / Common Pathway of Fibrin Clot Formation / platelet alpha granule lumen / blood coagulation / Platelet degranulation / : ...protein-glutamine gamma-glutamyltransferase / protein-glutamine gamma-glutamyltransferase activity / transferase complex / peptide cross-linking / blood coagulation, fibrin clot formation / Common Pathway of Fibrin Clot Formation / platelet alpha granule lumen / blood coagulation / Platelet degranulation / : / blood microparticle / Interleukin-4 and Interleukin-13 signaling / extracellular space / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() synthetic construct (others) | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Stieler, M. / Heine, A. / Klebe, G. | |||||||||
Funding support | ![]()
| |||||||||
![]() | ![]() Title: FXIIIa in complex with the inhibitor ZED2369 Authors: Stieler, M. / Heine, A. / Klebe, G. #1: ![]() Title: Structure of active coagulation factor XIII triggered by calcium binding: basis for the design of next-generation anticoagulants. Authors: Stieler, M. / Weber, J. / Hils, M. / Kolb, P. / Heine, A. / Buechold, C. / Pasternack, R. / Klebe, G. | |||||||||
History |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 531.6 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 433.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 479.1 KB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 493.6 KB | Display | |
Data in XML | ![]() | 47.9 KB | Display | |
Data in CIF | ![]() | 65.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4ktyS S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
Deposited unit | ![]()
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 | ![]()
| ||||||||
2 | ![]()
| ||||||||
Unit cell |
|
-
Components
#1: Protein | Mass: 84206.039 Da / Num. of mol.: 2 / Mutation: T649I, Q651E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P00488, protein-glutamine gamma-glutamyltransferase #2: Protein/peptide | Mass: 1051.259 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-CA / #4: Chemical | #5: Water | ChemComp-HOH / | Has protein modification | Y | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.67 Å3/Da / Density % sol: 53.9 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: 170 mM ammonium sulfate, 85 mM sodium cacodylate, 25.5 % PEG8000, 15 % glycerol |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 22, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.91841 Å / Relative weight: 1 |
Reflection | Resolution: 2.92→48.11 Å / Num. obs: 37113 / % possible obs: 97.2 % / Observed criterion σ(I): -3 / Redundancy: 2.2 % / Rsym value: 0.087 / Net I/σ(I): 10.7 |
Reflection shell | Resolution: 2.92→3.09 Å / Redundancy: 2.2 % / Rmerge(I) obs: 0.46 / Mean I/σ(I) obs: 2 / % possible all: 96.6 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Starting model: 4KTY Resolution: 2.92→17.706 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.58
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.92→17.706 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|