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Yorodumi- PDB-4bvc: Identification of small molecule inhibitors selective for apo(a) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bvc | ||||||
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Title | Identification of small molecule inhibitors selective for apo(a) kringles KIV-7, KIV-10 and KV. | ||||||
Components | APOLIPOPROTEIN(A) | ||||||
Keywords | HYDROLASE / LIPOPROTEIN(A) / CARDIOVASCULAR DISEASE / DRUG DISCOVERY / OPTICAL BIOSENSORS | ||||||
Function / homology | Function and homology information plasma lipoprotein particle / LDL remodeling / blood circulation / lipid transport / endopeptidase inhibitor activity / apolipoprotein binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / fibronectin binding / lipid metabolic process / heparin binding ...plasma lipoprotein particle / LDL remodeling / blood circulation / lipid transport / endopeptidase inhibitor activity / apolipoprotein binding / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / fibronectin binding / lipid metabolic process / heparin binding / endopeptidase activity / serine-type endopeptidase activity / signaling receptor binding / proteolysis / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Sandmark, J. / Althage, M. / Andersson, G.M.K. / Antonsson, T. / Blaho, S. / Bodin, C. / Bostrom, J. / Chen, Y. / Dahlen, A. / Eriksson, P.O. ...Sandmark, J. / Althage, M. / Andersson, G.M.K. / Antonsson, T. / Blaho, S. / Bodin, C. / Bostrom, J. / Chen, Y. / Dahlen, A. / Eriksson, P.O. / Evertsson, E. / Fex, T. / Fjellstrom, O. / Gustafsson, D. / Hallberg, C. / Hicks, R. / Jarkvist, E. / Johansson, C. / Kalies, I. / Kang, D. / Svalstedt Karlsson, B. / Kartberg, F. / Legnehed, A. / Lindqvist, A.M. / Martinsson, S.A. / Moberg, A. / Petersson, A.U. / Ridderstrom, M. / Thelin, A. / Tigerstrom, A. / Vinblad, J. / Xu, B. / Knecht, W. | ||||||
Citation | Journal: To be Published Title: Small Molecules Used to Decipher the Pathophysiological Roles of the Kringle Domains Kiv-7, - 10 and Kv of Apolipoprotein(A) Authors: Sandmark, J. / Althage, M. / Andersson, G.M.K. / Antonsson, T. / Blaho, S. / Bodin, C. / Bostrom, J. / Chen, Y. / Dahlen, A. / Eriksson, P.O. / Evertsson, E. / Fex, T. / Fjellstrom, O. / ...Authors: Sandmark, J. / Althage, M. / Andersson, G.M.K. / Antonsson, T. / Blaho, S. / Bodin, C. / Bostrom, J. / Chen, Y. / Dahlen, A. / Eriksson, P.O. / Evertsson, E. / Fex, T. / Fjellstrom, O. / Gustafsson, D. / Hallberg, C. / Hicks, R. / Jarkvist, E. / Johansson, C. / Kalies, I. / Kang, D. / Svalstedt Karlsson, B. / Kartberg, F. / Legnehed, A. / Lindqvist, A.M. / Martinsson, S.A. / Moberg, A. / Petersson, A.U. / Ridderstrom, M. / Thelin, A. / Tigerstrom, A. / Vinblad, J. / Xu, B. / Knecht, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bvc.cif.gz | 33.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bvc.ent.gz | 21.6 KB | Display | PDB format |
PDBx/mmJSON format | 4bvc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bvc_validation.pdf.gz | 740.1 KB | Display | wwPDB validaton report |
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Full document | 4bvc_full_validation.pdf.gz | 740.2 KB | Display | |
Data in XML | 4bvc_validation.xml.gz | 7.2 KB | Display | |
Data in CIF | 4bvc_validation.cif.gz | 9.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/4bvc ftp://data.pdbj.org/pub/pdb/validation_reports/bv/4bvc | HTTPS FTP |
-Related structure data
Related structure data | 4bv5C 4bv7C 4bvdC 4bvvC 4bvwC 3kivS C: citing same article (ref.) S: Starting model for refinement |
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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
#1: Protein | Mass: 9156.078 Da / Num. of mol.: 1 / Fragment: KRINGLE DOMAIN IV-10, RESIDUES 4123-4201 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PPICZALPHAC / Production host: KOMAGATAELLA PASTORIS (fungus) / Strain (production host): X-33 References: UniProt: P08519, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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#2: Chemical | ChemComp-CL / |
#3: Chemical | ChemComp-BV5 / |
#4: Chemical | ChemComp-PEG / |
#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: 1.7 Å3/Da / Density % sol: 28 % / Description: NONE |
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Crystal grow | pH: 8.5 / Details: 8% PEG8000, 0.1M TRIS PH8.5, 0.2M LISO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-E+ / Wavelength: 1.5418 |
Detector | Type: RIGAKU CCD-A200-CU / Detector: CCD / Date: Sep 12, 2012 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→24.6 Å / Num. obs: 8006 / % possible obs: 93 % / Observed criterion σ(I): 2 / Redundancy: 5.9 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 13 |
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 1.7 / % possible all: 57 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3KIV Resolution: 1.6→23.61 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.925 / Cross valid method: THROUGHOUT / ESU R: 0.115 / ESU R Free: 0.107 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 11.817 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→23.61 Å
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