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Open data
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Basic information
Entry | Database: PDB / ID: 1iqn | ||||||
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Title | Human coagulation factor Xa in complex with M55192 | ||||||
![]() | (coagulation Factor Xa) x 2 | ||||||
![]() | HYDROLASE / SERINE PROTEASE / BLOOD COAGULATION FACTOR / COMPLEX | ||||||
Function / homology | ![]() coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins ...coagulation factor Xa / Defective factor IX causes thrombophilia / Defective cofactor function of FVIIIa variant / Defective F9 variant does not activate FX / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of TOR signaling / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / phospholipid binding / Golgi lumen / blood coagulation / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / calcium ion binding / proteolysis / extracellular space / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Shiromizu, I. / Matsusue, T. | ||||||
![]() | ![]() Title: Factor Xa Specific Inhibitor that Induces the Novel Binding Model in Complex with Human Fxa Authors: Matsusue, T. / Shiromizu, I. / Okamoto, A. / Nakayama, K. / Nishida, H. / Mukaihira, T. / Miyazaki, Y. / Saitou, F. / Morishita, H. / Ohnishi, S. / Mochizuki, H. #1: ![]() Title: Structure of Human Des(1-45) Factor Xa at 2.2 A Resolution Authors: Padmanabhan, K. / Padmanabhan, K.P. / Tulinsky, A. / Park, C.H. / Bode, W. / Huber, R. / Blankenship, D.T. / Cardin, A.D. / Kisiel, W. #2: ![]() Title: X-Ray Structure of Active Site-Inhibited Clotting Factor Xa. Implications for Drug Design and Substrate Recognition Authors: Brandstetter, H. / Kuhne, A. / Bode, W. / Huber, R. / Von Der Saal, W. / Wirthensohn, K. / Engh, R.A. #3: ![]() Title: Autoproteolysis or Plasmin-Mediated Cleavage of Factor Xaalpha Exposes a Plasminogen Binding Site and Inhibits Coagulation Authors: Pryzdial, E.L. / Kessler, G.E. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 73.7 KB | Display | ![]() |
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PDB format | ![]() | 53.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1iqeC ![]() 1iqfC ![]() 1iqgC ![]() 1iqhC ![]() 1iqiC ![]() 1iqjC ![]() 1iqkC ![]() 1iqlC ![]() 1iqmC C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 26604.297 Da / Num. of mol.: 1 / Fragment: heavy chain, catalytic domain (residues 235-469) / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 10533.713 Da / Num. of mol.: 1 Fragment: light chain, epidermal growth factor like domain (residues 84-179) Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-XMC / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.15 Å3/Da / Density % sol: 42.85 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: PEG1500, calcium chloride, M55192, tris-HCl, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 27, 1999 / Details: mirrors |
Radiation | Monochromator: Yale Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Highest resolution: 2.6 Å / Num. obs: 8510 / % possible obs: 82.1 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.036 |
Reflection shell | Resolution: 2.6→2.7 Å / Rmerge(I) obs: 0.067 / % possible all: 64.7 |
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Processing
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Refinement | Method to determine structure: ![]()
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Displacement parameters | Biso mean: 31.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.6→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.6→2.67 Å / Rfactor Rfree error: 0.034
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