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- PDB-4crg: Creating novel F1 inhibitors through fragment based lead generati... -
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Open data
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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 | ||||||
![]() | COAGULATION FACTOR XI | ||||||
![]() | HYDROLASE | ||||||
Function / homology | ![]() 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 / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | 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. | ||||||
![]() | ![]() 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. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 116.1 KB | Display | ![]() |
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PDB format | ![]() | 96.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 995.2 KB | Display | ![]() |
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Full document | ![]() | 995.2 KB | Display | |
Data in XML | ![]() | 14.9 KB | Display | |
Data in CIF | ![]() | 23.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4cr5C ![]() 4cr9C ![]() 4craC ![]() 4crbC ![]() 4crcC ![]() 4crdC ![]() 4creC ![]() 4crfC 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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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.) ![]() ![]() | ||||||||
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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: ![]() |
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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: ![]() ![]() ![]() |
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 |
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Processing
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Refinement | Method to determine structure: ![]() 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 } |