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Yorodumi- PDB-4crg: Creating novel F1 inhibitors through fragment based lead generati... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4crg | ||||||
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Title | Creating novel F1 inhibitors through fragment based lead generation and structure aided drug design | ||||||
Components | COAGULATION FACTOR XIFactor XI | ||||||
Keywords | HYDROLASE | ||||||
Function / homology | Function and homology information coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space ...coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space / extracellular exosome / extracellular region / membrane / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å | ||||||
Authors | Sandmark, J. / Oster, L. / Fjellstrom, O. / Akkaya, S. / Beisel, H.G. / Eriksson, P.O. / Erixon, K. / Gustafsson, D. / Jurva, U. / Kang, D. ...Sandmark, J. / Oster, L. / Fjellstrom, O. / Akkaya, S. / Beisel, H.G. / Eriksson, P.O. / Erixon, K. / Gustafsson, D. / Jurva, U. / Kang, D. / Karis, D. / Knecht, W. / Nerme, V. / Nilsson, I. / Olsson, T. / Redzic, A. / Roth, R. / Tigerstrom, A. | ||||||
Citation | Journal: Plos One / Year: 2015 Title: Creating Novel Activated Factor Xi Inhibitors Through Fragment Based Lead Generation and Structure Aided Drug Design. Authors: Fjellstrom, O. / Akkaya, S. / Beisel, H. / Eriksson, P. / Erixon, K. / Gustafsson, D. / Jurva, U. / Kang, D. / Karis, D. / Knecht, W. / Nerme, V. / Nilsson, I. / Olsson, T. / Redzic, A. / ...Authors: Fjellstrom, O. / Akkaya, S. / Beisel, H. / Eriksson, P. / Erixon, K. / Gustafsson, D. / Jurva, U. / Kang, D. / Karis, D. / Knecht, W. / Nerme, V. / Nilsson, I. / Olsson, T. / Redzic, A. / Roth, R. / Sandmark, J. / Tigerstrom, A. / Oster, L. | ||||||
History |
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Remark 700 | SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" IN EACH CHAIN ON SHEET RECORDS BELOW ... SHEET DETERMINATION METHOD: DSSP THE SHEETS PRESENTED AS "AB" 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 | 4crg.cif.gz | 116.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4crg.ent.gz | 96.6 KB | Display | PDB format |
PDBx/mmJSON format | 4crg.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cr/4crg ftp://data.pdbj.org/pub/pdb/validation_reports/cr/4crg | HTTPS FTP |
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-Related structure data
Related structure data | 4cr5C 4cr9C 4craC 4crbC 4crcC 4crdC 4creC 4crfC 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 26752.369 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 388-625 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P03951, coagulation factor XIa | ||||||||
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#2: Chemical | ChemComp-GOL / #3: Chemical | ChemComp-J4X / | #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | Sequence details | MUTANT, S75A K78A T97A C123S | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.75 Å3/Da / Density % sol: 55.28 % / Description: NONE |
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Crystal grow | pH: 8.5 Details: 2M AMMONIUM SULFATE, 0.1M TRIS-CL PH 8.5, 0.2M NACL |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.94 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Feb 15, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.94 Å / Relative weight: 1 |
Reflection | Resolution: 1.25→49.3 Å / Num. obs: 75396 / % possible obs: 92.8 % / Observed criterion σ(I): 2 / Redundancy: 5.2 % / Biso Wilson estimate: 13.6 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.8 |
Reflection shell | Resolution: 1.25→1.33 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.8 / % possible all: 75 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→49.35 Å / Cor.coef. Fo:Fc: 0.9336 / Cor.coef. Fo:Fc free: 0.9247 / SU R Cruickshank DPI: 0.043 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.045 / SU Rfree Blow DPI: 0.047 / SU Rfree Cruickshank DPI: 0.045 Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY. THE LIGAND J4X IS PLACED IN THE DENSITY IN TWO DIFFERENT ORIENTATIONS
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Displacement parameters | Biso mean: 21.11 Å2
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Refinement step | Cycle: LAST / Resolution: 1.25→49.35 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.25→1.28 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: -28.5217 Å / Origin y: -42.8729 Å / Origin z: -10.8567 Å
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Refinement TLS group | Selection details: { A|370 - A|607 } |