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Open data
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Basic information
Entry | Database: PDB / ID: 4lb9 | ||||||
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Title | X-ray study of human serum albumin complexed with etoposide | ||||||
![]() | SERUM ALBUMIN | ||||||
![]() | TRANSPORT PROTEIN / PLASMA PROTEIN / CANCER / ONCOLOGY DRUG COMPLEX | ||||||
Function / homology | ![]() cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME ...cellular response to calcium ion starvation / exogenous protein binding / Ciprofloxacin ADME / enterobactin binding / Heme biosynthesis / HDL remodeling / negative regulation of mitochondrial depolarization / Prednisone ADME / Heme degradation / Aspirin ADME / antioxidant activity / toxic substance binding / small molecule 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) / pyridoxal phosphate binding / Platelet degranulation / 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 | ![]() | ||||||
Method | ![]() | ||||||
![]() | Wang, Z. / Ho, J.X. / Ruble, J. / Rose, J.P. / Carter, D.C. | ||||||
![]() | ![]() 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: ![]() Year: 2010 Title: Crystallographic survey of albumin drug interaction and preliminary applications in cancer chemotherapy Authors: Carter, D.C. #2: ![]() 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: ![]() Title: Erratum. Atomic Structure and Chemistry of Human Serum Albumin Authors: Ho, X.M. / Carter, D.C. #5: ![]() Title: Atomic structure and chemistry of human serum albumin. Authors: He, X.M. / Carter, D.C. #6: ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 125.8 KB | Display | ![]() |
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PDB format | ![]() | 104 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 781.3 KB | Display | ![]() |
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Full document | ![]() | 795.5 KB | Display | |
Data in XML | ![]() | 24.1 KB | Display | |
Data in CIF | ![]() | 32.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components on special symmetry positions |
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Components
#1: Protein | Mass: 66571.219 Da / Num. of mol.: 1 / Fragment: UNP residues 25-609 / Source method: isolated from a natural source / Source: (natural) ![]() | ||||
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#2: Chemical | ChemComp-MYR / #3: Chemical | ChemComp-EVP / ( | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.41 Å3/Da / Density % sol: 48.89 % |
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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: ![]() | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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: 15546 / % possible obs: 86.6 % / Rmerge(I) obs: 0.068 / Χ2: 1.321 / Net I/σ(I): 12.7 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell |
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Processing
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Refinement | Method to determine structure: MERLOT / Resolution: 2.7→25.679 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.41 / σ(F): 1.34 / Phase error: 26.86 / 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: 84.35 Å2 / Biso mean: 33.1846 Å2 / Biso min: 10.67 Å2 | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.7→25.679 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 5
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