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Open data
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Basic information
Entry | Database: PDB / ID: 4y71 | ||||||
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Title | Factor Xa complex with GTC000398 | ||||||
![]() | (Coagulation factor X) x 2 | ||||||
![]() | HYDROLASE / Inhibitor | ||||||
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 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
Model details | Chains A & B are disulfide bonded together | ||||||
![]() | Convery, M.A. / Young, R.J. / Senger, S. / Hamblin, J.N. / Chan, C. / Toomey, J.R. / Watson, N.S. | ||||||
![]() | ![]() Title: Factor Xa complex with GTC000398 Authors: Convery, M.A. / Young, R.J. / Senger, S. / Hamblin, J.N. / Chan, C. / Toomey, J.R. / Watson, N.S. #1: ![]() Title: Factor Xa inhibitors: S1 binding interactions of a series of N-{(3S)-1-[(1S)-1-methyl-2-morpholin-4-yl-2-oxoethyl]-2-oxopyrrolidin-3-yl}sulfonamides. Authors: Chan, C. / Borthwick, A.D. / Brown, D. / Burns-Kurtis, C.L. / Campbell, M. / Chaudry, L. / Chung, C.W. / Convery, M.A. / Hamblin, J.N. / Johnstone, L. / Kelly, H.A. / Kleanthous, S. / ...Authors: Chan, C. / Borthwick, A.D. / Brown, D. / Burns-Kurtis, C.L. / Campbell, M. / Chaudry, L. / Chung, C.W. / Convery, M.A. / Hamblin, J.N. / Johnstone, L. / Kelly, H.A. / Kleanthous, S. / Patikis, A. / Patel, C. / Pateman, A.J. / Senger, S. / Shah, G.P. / Toomey, J.R. / Watson, N.S. / Weston, H.E. / Whitworth, C. / Young, R.J. / Zhou, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 80.6 KB | Display | ![]() |
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PDB format | ![]() | 57.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1 MB | Display | ![]() |
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Full document | ![]() | 1 MB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 21 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2j94C ![]() 2j95C ![]() 4y76C ![]() 4y79C ![]() 1ezqS S: Starting model for refinement 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: 28550.596 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() |
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#2: Protein | Mass: 15210.793 Da / Num. of mol.: 1 / Fragment: UNP residues 46-179 / Source method: isolated from a natural source / Source: (natural) ![]() |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-48W / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.87 Å3/Da / Density % sol: 34.22 % / Description: needle-shaped (200 x 50 x 50 um) |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 16 - 20 % PEG 6000, 50 mM MES-NaOH (pH 5.7-6.0), 5 mM calcium chloride, 50 mM sodium chloride PH range: 5.7 - 6.0 |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Oct 4, 2001 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.939 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.8→20 Å / Num. obs: 30525 / % possible obs: 99.3 % / Redundancy: 3.95 % / Rmerge(I) obs: 0.1 / Χ2: 0.991 / Net I/av σ(I): 12.167 / Net I/σ(I): 9.1 / Num. measured all: 118610 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1ezq Resolution: 1.8→19.92 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 2.889 / SU ML: 0.09 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.132 / ESU R Free: 0.13 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 102.13 Å2 / Biso mean: 34.74 Å2 / Biso min: 14.51 Å2
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Refinement step | Cycle: final / Resolution: 1.8→19.92 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.801→1.847 Å / Total num. of bins used: 20
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