+Open data
-Basic information
Entry | Database: PDB / ID: 4lb2 | ||||||
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Title | X-ray study of human serum albumin complexed with idarubicin | ||||||
Components | SERUM ALBUMIN | ||||||
Keywords | TRANSPORT PROTEIN / PLASMA PROTEIN / CANCER / ONCOLOGY DRUG COMPLEX | ||||||
Function / homology | Function and homology information exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / cellular response to calcium ion starvation / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / cellular response to calcium ion starvation / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / Scavenging of heme from plasma / Recycling of bile acids and salts / cellular response to starvation / platelet alpha granule lumen / fatty acid binding / Post-translational protein phosphorylation / Cytoprotection by HMOX1 / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / Platelet degranulation / pyridoxal phosphate binding / protein-folding chaperone binding / blood microparticle / copper ion binding / endoplasmic reticulum lumen / Golgi apparatus / endoplasmic reticulum / protein-containing complex / DNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.8 Å | ||||||
Authors | Wang, Z. / Ho, J.X. / Ruble, J. / Rose, J.P. / Carter, D.C. | ||||||
Citation | Journal: Biochim.Biophys.Acta / Year: 2013 Title: Structural studies of several clinically important oncology drugs in complex with human serum albumin. Authors: Wang, Z.M. / Ho, J.X. / Ruble, J.R. / Rose, J. / Ruker, F. / Ellenburg, M. / Murphy, R. / Click, J. / Soistman, E. / Wilkerson, L. / Carter, D.C. #1: Journal: Burgers medicinal chemistry drug design and development, 7th edition Year: 2010 Title: Crystallographic survey of albumin drug interaction and preliminary applications in cancer chemotherapy Authors: Carter, D.C. #2: Journal: Adv.Protein Chem. / Year: 1994 Title: Structure of Serum Albumin Authors: Carter, D.C. / Ho, J.X. #3: Journal: Eur.J.Biochem. / Year: 1994 Title: Preliminary crystallographic studies of four crystal forms of serum albumin. Authors: Carter, D.C. / Chang, B. / Ho, J.X. / Keeling, K. / Krishnasami, Z. #4: Journal: Nature / Year: 1993 Title: Erratum. Atomic Structure and Chemistry of Human Serum Albumin Authors: Ho, X.M. / Carter, D.C. #5: Journal: Nature / Year: 1992 Title: Atomic structure and chemistry of human serum albumin. Authors: He, X.M. / Carter, D.C. #6: Journal: Science / Year: 1990 Title: Structure of Human Serum Albumin Authors: Carter, D.C. / Ho, X.M. #7: Journal: Science / Year: 1989 Title: Three-dimensional structure of human serum albumin. Authors: Carter, D.C. / He, X.M. / Munson, S.H. / Twigg, P.D. / Gernert, K.M. / Broom, M.B. / Miller, T.Y. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4lb2.cif.gz | 234.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4lb2.ent.gz | 196.8 KB | Display | PDB format |
PDBx/mmJSON format | 4lb2.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4lb2_validation.pdf.gz | 1.5 MB | Display | wwPDB validaton report |
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Full document | 4lb2_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 4lb2_validation.xml.gz | 41.9 KB | Display | |
Data in CIF | 4lb2_validation.cif.gz | 56.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lb/4lb2 ftp://data.pdbj.org/pub/pdb/validation_reports/lb/4lb2 | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain: (Details: chain B and segid HSB) NCS domain segments: (Selection details: chain 'B' and segid 'HSB ') |
-Components
#1: Protein | Mass: 66571.219 Da / Num. of mol.: 2 / Fragment: UNP residues 25-609 / Source method: isolated from a natural source / Source: (natural) Homo sapiens (human) / References: UniProt: P02768 #2: Chemical | ChemComp-DM5 / #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.28 Å3/Da / Density % sol: 46.11 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG 3350, POTASSIUM PHOSPHATE, Crystals of the complexes were obtained by standard vapor equilibration methods with conditions optimized by screens varying protein concentration, pH, drug ...Details: PEG 3350, POTASSIUM PHOSPHATE, Crystals of the complexes were obtained by standard vapor equilibration methods with conditions optimized by screens varying protein concentration, pH, drug molar ratios, centered on the original crystallization hit using protocols described previously for the monoclinic [Carter, et al., Eur. J. Biochemistry (1994) 226: 1049-1052] and triclinic [Sugo, et al., Protein Eng (1999) 12: 439-446] crystal forms., pH 7.5, vapor diffusion, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU300 / Wavelength: 1.5418 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jan 1, 2003 / Details: CONFOCAL OPTICS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: CONFOCAL OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 2.7→30 Å / Num. obs: 31105 / % possible obs: 96.2 % / Rmerge(I) obs: 0.075 / Χ2: 4.351 / Net I/σ(I): 13.8 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→28.163 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.3 / σ(F): 1.97 / Phase error: 26.37 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 103.23 Å2 / Biso mean: 43.1098 Å2 / Biso min: 12.8 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.8→28.163 Å
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Refine LS restraints |
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Refine LS restraints NCS | Number: 5405 / Type: POSITIONAL / Rms dev position: 12.635 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 10
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