+Open data
-Basic information
Entry | Database: PDB / ID: 4y7a | ||||||
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Title | Factor Xa complex with GTC000422 | ||||||
Components | (Coagulation factor ...) x 2 | ||||||
Keywords | HYDROLASE / Inhibitor | ||||||
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: 1.99 Å | ||||||
Model details | Chains A & B are disulfide bonded together | ||||||
Authors | Convery, M.A. / Young, R.J. / Senger, S. / Hamblin, J.N. / Chan, C. / Toomey, J.R. / Watson, N.S. | ||||||
Citation | Journal: to be published Title: Factor Xa complex with GTC000422 Authors: Convery, M.A. / Young, R.J. / Senger, S. / Hamblin, J.N. / Chan, C. / Toomey, J.R. / Watson, N.S. #1: Journal: J. Med. Chem. / Year: 2007 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4y7a.cif.gz | 81.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4y7a.ent.gz | 57.4 KB | Display | PDB format |
PDBx/mmJSON format | 4y7a.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y7/4y7a ftp://data.pdbj.org/pub/pdb/validation_reports/y7/4y7a | HTTPS FTP |
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-Related structure data
Related structure data | 2j94C 2j95C 4y76C 4y79C 1ezqS 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
-Coagulation factor ... , 2 types, 2 molecules AB
#1: 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 |
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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) Homo sapiens (human) / References: UniProt: P00742, coagulation factor Xa |
-Non-polymers , 4 types, 218 molecules
#3: Chemical | ChemComp-CA / |
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#4: Chemical | ChemComp-MG / |
#5: Chemical | ChemComp-987 / |
#6: 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: 1.93 Å3/Da / Density % sol: 36.22 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop Details: 18% PEG 6000, 100 mM MES PH 5.75, 10 mM calcium chloride |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX9.6 |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Mar 28, 2001 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.99→26.63 Å / Num. obs: 23605 / % possible obs: 99.3 % / Redundancy: 4 % / Rmerge(I) obs: 0.085 / Net I/σ(I): 11.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ezq Resolution: 1.99→20 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.938 / SU B: 4.34 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.173 / ESU R Free: 0.161 / 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: 108.1 Å2 / Biso mean: 35.769 Å2 / Biso min: 16.62 Å2
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Refinement step | Cycle: final / Resolution: 1.99→20 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.992→2.043 Å / Total num. of bins used: 20
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