+Open data
-Basic information
Entry | Database: PDB / ID: 2bqw | ||||||
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Title | CRYSTAL STRUCTURE OF FACTOR XA IN COMPLEX WITH COMPOUND 45 | ||||||
Components |
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Keywords | HYDROLASE / BLOOD COAGULATION / BLOOD COAGULATION FACTOR / CALCIUM-BINDING / EGF-LIKE DOMAIN / GAMMA-CARBOXYGLUTAMIC ACID / GLYCOPROTEIN / HYDROXYLATION / PLASMA / POLYMORPHISM / PROTEIN INHIBITOR COMPLEX / SERINE PROTEINASE / SERINE PROTEASE / VITAMIN K / ZYMOGEN | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.95 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 | 2bqw.cif.gz | 76.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bqw.ent.gz | 55.6 KB | Display | PDB format |
PDBx/mmJSON format | 2bqw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2bqw_validation.pdf.gz | 741.9 KB | Display | wwPDB validaton report |
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Full document | 2bqw_full_validation.pdf.gz | 752.8 KB | Display | |
Data in XML | 2bqw_validation.xml.gz | 15.3 KB | Display | |
Data in CIF | 2bqw_validation.cif.gz | 21 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bq/2bqw ftp://data.pdbj.org/pub/pdb/validation_reports/bq/2bqw | HTTPS FTP |
-Related structure data
Related structure data | 2bohC 2bq6C 2bq7C 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: 5617.314 Da / Num. of mol.: 1 / Fragment: DES-GLA LIGHT CHAIN, RESIDUES 126-177 / 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: 28220.969 Da / Num. of mol.: 1 / Fragment: HEAVY CHAIN, RESIDUES 220-468 / 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-IIE / |
#5: Water | ChemComp-HOH / |
-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: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jun 11, 2002 / Details: OSMIC MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.95→60 Å / Num. obs: 6939 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 4.8 % / Biso Wilson estimate: 23.9 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 13.7 |
Reflection shell | Resolution: 2.95→3 Å / Redundancy: 4.86 % / Rmerge(I) obs: 0.31 / Mean I/σ(I) obs: 5.4 / % possible all: 97.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1LPG Resolution: 2.95→200 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 Details: EGF1 DOMAIN PRESENT BUT NOT VISIBLE IN THE ELECTRON DENSITY MAPS
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Solvent computation | Solvent model: MASK / Bsol: 28.2913 Å2 / ksol: 0.346487 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.9 Å2
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Refinement step | Cycle: LAST / Resolution: 2.95→200 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.95→3.08 Å / Total num. of bins used: 8 /
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Xplor file | Serial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: AVENTIS.TOP |