+Open data
-Basic information
Entry | Database: PDB / ID: 2boh | ||||||
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Title | Crystal structure of factor Xa in complex with compound "1" | ||||||
Components | (COAGULATION FACTOR XA) x 2 | ||||||
Keywords | HYDROLASE/INHIBITOR / COMPLEX (HYDROLASE-INHIBITOR) / PROTEIN-INHIBITOR COMPLEX / BLOOD COAGULATION FACTOR / SERINE PROTEINASE / RATIONAL DRUG DESIGN / CALCIUM-BINDING / EGF-LIKE DOMAIN / GAMMA-CARBOXYGLUTAMIC ACID / GLYCOPROTEIN / HYDROLASE / HYDROXYLATION / PLASMA / POLYMORPHISM / PROTEASE / SERINE PROTEASE / VITAMIN K / ZYMOGEN / HYDROLASE-INHIBITOR 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 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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Nazare, M. / Will, D.W. / Matter, H. / Schreuder, H. / Ritter, K. / Urmann, M. / Essrich, M. / Bauer, A. / Wagner, M. / Czech, J. ...Nazare, M. / Will, D.W. / Matter, H. / Schreuder, H. / Ritter, K. / Urmann, M. / Essrich, M. / Bauer, A. / Wagner, M. / Czech, J. / Laux, V. / Wehner, V. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2005 Title: Probing the Subpockets of Factor Xa Reveals Two Binding Modes for Inhibitors Based on a 2-Carboxyindole Scaffold: A Study Combining Structure-Activity Relationship and X-Ray Crystallography. Authors: Nazare, M. / Will, D.W. / Matter, H. / Schreuder, H. / Ritter, K. / Urmann, M. / Essrich, M. / Bauer, A. / Wagner, M. / Czech, J. / Lorenz, M. / Laux, V. / Wehner, V. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "BB" IN EACH CHAIN ON SHEET RECORDS BELOW IS ACTUALLY AN 6-STRANDED BARREL THIS IS REPRESENTED BY A 7-STRANDED SHEET IN WHICH THE FIRST AND LAST STRANDS ARE IDENTICAL |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2boh.cif.gz | 81.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2boh.ent.gz | 58.2 KB | Display | PDB format |
PDBx/mmJSON format | 2boh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2boh_validation.pdf.gz | 755.7 KB | Display | wwPDB validaton report |
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Full document | 2boh_full_validation.pdf.gz | 763.1 KB | Display | |
Data in XML | 2boh_validation.xml.gz | 16.4 KB | Display | |
Data in CIF | 2boh_validation.cif.gz | 23.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bo/2boh ftp://data.pdbj.org/pub/pdb/validation_reports/bo/2boh | HTTPS FTP |
-Related structure data
Related structure data | 2bq6C 2bq7C 2bqwC 1lpgS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15210.793 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN, RESIDUES 126-234 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Tissue: BLOOD / References: UniProt: P00742, coagulation factor Xa |
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#2: Protein | Mass: 28550.596 Da / Num. of mol.: 1 / Fragment: LIGHT CHAIN, RESIDUES 235-488 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / Tissue: BLOOD / References: UniProt: P00742, coagulation factor Xa |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-IIA / |
#5: Water | ChemComp-HOH / |
Compound details | FUNCTION: FACTOR XA CONVERTS PROTHROMBI |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.4 Å3/Da / Density % sol: 49 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 5.7 Details: PEG600, MES, CACL2, PH 5.7, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298.0 K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.934 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Jun 6, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.934 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→50 Å / Num. obs: 16670 / % possible obs: 98.8 % / Observed criterion σ(I): -3 / Redundancy: 4.4 % / Biso Wilson estimate: 41.3 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 11.7 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 5 / % possible all: 99.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LPG Resolution: 2.2→50 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
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Solvent computation | Solvent model: MASK / Bsol: 54.2666 Å2 / ksol: 0.371923 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.8 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→50 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.26 Å / Total num. of bins used: 13 /
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: AVENTIS.TOP |