+Open data
-Basic information
Entry | Database: PDB / ID: 1ioe | ||||||
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Title | Human coagulation factor Xa in complex with M55532 | ||||||
Components | (COAGULATION FACTOR XA) x 2 | ||||||
Keywords | HYDROLASE / serine protease / blood coagulation factor / complex | ||||||
Function / homology | Function and homology information 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 leukocyte chemotaxis / 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 ...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 leukocyte chemotaxis / 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.9 Å | ||||||
Authors | Shiromizu, I. / Matsusue, T. | ||||||
Citation | Journal: To be Published 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: Journal: J.Mol.Biol. / Year: 1993 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: Journal: J.Biol.Chem. / Year: 1996 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: Journal: J.Biol.Chem. / Year: 1996 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ioe.cif.gz | 71 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ioe.ent.gz | 52 KB | Display | PDB format |
PDBx/mmJSON format | 1ioe.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1ioe_validation.pdf.gz | 469.5 KB | Display | wwPDB validaton report |
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Full document | 1ioe_full_validation.pdf.gz | 488.5 KB | Display | |
Data in XML | 1ioe_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 1ioe_validation.cif.gz | 14.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/io/1ioe ftp://data.pdbj.org/pub/pdb/validation_reports/io/1ioe | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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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) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa |
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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) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-XMA / (-)- |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.14 Å3/Da / Density % sol: 42.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.2 Details: PEG1500, CALCIUM CHLORIDE, M55532,TRIS-HCL, pH 7.20, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Dec 18, 1998 / 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 | Resolution: 2.9→20 Å / Num. obs: 5790 / % possible obs: 81.9 % / Observed criterion σ(I): 1 / Rmerge(I) obs: 0.0815 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.9→8 Å / Rfactor Rfree error: 0.012 / σ(F): 0
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Displacement parameters | Biso mean: 29.7 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine analyze | Luzzati coordinate error obs: 0.33 Å / Luzzati d res low obs: 5 Å / Luzzati sigma a obs: 0.37 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.9→8 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.9→3.07 Å / Rfactor Rfree error: 0.042
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