+Open data
-Basic information
Entry | Database: PDB / ID: 1lpg | ||||||
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Title | CRYSTAL STRUCTURE OF FXA IN COMPLEX WITH 79. | ||||||
Components | (Blood coagulation factor Xa) x 2 | ||||||
Keywords | HYDROLASE / Protein inhibitor complex / blood coagulation factor / serine proteinase | ||||||
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 Å | ||||||
Authors | Schreuder, H.A. / Brachvogel, V. / Liesum, A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2002 Title: Design and Quantitative Structure-Activity relationship of 3-amidinobenzyl-1H-indole-2-carboxamides as potent, nonchiral, and selective inhibitors of blood coagulation factor Xa. Authors: Matter, H. / Defossa, E. / Heinelt, U. / Blohm, P.M. / Schneider, D. / Mueller, A. / Herok, S. / Schreuder, H. / Liesum, A. / Brachvogel, B. / Loenze, P. / Walser, A. / Al-Obeidi, F. / Wildgoose, P. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1lpg.cif.gz | 75.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1lpg.ent.gz | 58.7 KB | Display | PDB format |
PDBx/mmJSON format | 1lpg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lp/1lpg ftp://data.pdbj.org/pub/pdb/validation_reports/lp/1lpg | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15210.793 Da / Num. of mol.: 1 / Fragment: light chain / 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: 28550.596 Da / Num. of mol.: 1 / 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-IMA / [ |
#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: 2.2 Å3/Da / Density % sol: 43.67 % | |||||||||||||||||||||||||||||||||||||||||||||||||
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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 298.0K | |||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 19 ℃ / PH range low: 7 / PH range high: 5 | |||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.54128 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 2, 2000 / Details: graphite monochromator |
Radiation | Monochromator: Graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54128 Å / Relative weight: 1 |
Reflection | Resolution: 2→50 Å / Num. all: 20223 / Num. obs: 22200 / % possible obs: 91.1 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Rmerge(I) obs: 0.069 / Rsym value: 0.059 / Net I/σ(I): 14.3 |
Reflection shell | Resolution: 2→2.1 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.232 / Mean I/σ(I) obs: 3.4 / Num. unique all: 2092 / Rsym value: 0.324 / % possible all: 71 |
Reflection | *PLUS Num. obs: 20233 / Num. measured all: 70257 / Rmerge(I) obs: 0.059 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→50 Å / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): -3 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 29.2 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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Refinement | *PLUS Highest resolution: 2 Å / Rfactor Rfree: 0.286 / Rfactor Rwork: 0.197 | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||||||||||||
Refine LS restraints | *PLUS
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