[English] 日本語
Yorodumi- PDB-4bvw: Identification of small molecule inhibitors selective for apo(a) ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bvw | ||||||
---|---|---|---|---|---|---|---|
Title | Identification of small molecule inhibitors selective for apo(a) kringles KIV-7, KIV-10 and KV. | ||||||
Components | APOLIPOPROTEIN(A) | ||||||
Keywords | HYDROLASE / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 4bvw.cif.gz | 50.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb4bvw.ent.gz | 35.4 KB | Display | PDB format |
PDBx/mmJSON format | 4bvw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bvw_validation.pdf.gz | 463.8 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 4bvw_full_validation.pdf.gz | 464.8 KB | Display | |
Data in XML | 4bvw_validation.xml.gz | 10.5 KB | Display | |
Data in CIF | 4bvw_validation.cif.gz | 13.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bv/4bvw ftp://data.pdbj.org/pub/pdb/validation_reports/bv/4bvw | HTTPS FTP |
-Related structure data
Related structure data | 4bv5C 4bv7C 4bvcC 4bvdC 4bvvC 1i71S C: citing same article (ref.) S: Starting model for refinement |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
| ||||||||
Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (-1, 0.005047, 0.007257), Vector: |
-Components
#1: Protein | Mass: 11296.453 Da / Num. of mol.: 2 / Fragment: KRINGLE DOMAIN IV-7, RESIDUES 3781-3859 / 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 #2: Chemical | ChemComp-CL / #3: Chemical | #4: Chemical | ChemComp-EDO / | #5: Water | ChemComp-HOH / | Sequence details | N74A MUTATION. N-TERMINAL EXTENSION, PART OF THE ALPHA MATING FACTOR FROM THE EXPRESSION VECTOR, ...N74A MUTATION. N-TERMINAL EXTENSION, PART OF THE ALPHA MATING FACTOR FROM THE EXPRESSION | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.3 Å3/Da / Density % sol: 46 % / Description: NONE |
---|---|
Crystal grow | Details: 19% PEG 6000, 0.1 M NAOAC, 12% ETHYLENE GLYCOL, 1M LISO4 |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.873 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jun 20, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.873 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. obs: 10414 / % possible obs: 96.1 % / Observed criterion σ(I): 2 / Redundancy: 3.1 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 6.6 |
Reflection shell | Resolution: 2→2.05 Å / Redundancy: 3 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 1.9 / % possible all: 94.6 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1I71 Resolution: 2→24.68 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.919 / Cross valid method: THROUGHOUT / ESU R: 0.26 / ESU R Free: 0.203 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE N-TERMINAL EXTENSION ORIGINATING FROM THE EXPRESSION VECTOR WAS NOT MODELLED.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 17.229 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→24.68 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|