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Yorodumi- PDB-4bke: Recombinant human serum albumin with palmitic acid. Synthetic cat... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4bke | ||||||
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Title | Recombinant human serum albumin with palmitic acid. Synthetic cationic antimicrobial peptides bind with their hydrophobic parts to drug site II of human serum albumin | ||||||
Components | SERUM ALBUMIN | ||||||
Keywords | TRANSPORT PROTEIN / ALBUMIN BINDING / GROUP EPITOPE MAPPING / MOLECULAR DOCKING | ||||||
Function / homology | Function and homology information 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 / 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 | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | ||||||
Authors | Sivertsen, A. / Isaksson, J. / Leiros, H.-K.S. / Svenson, J. / Svendsen, J.-S. / Brandsdal, B.-O. | ||||||
Citation | Journal: Bmc Struct.Biol. / Year: 2014 Title: Synthetic Cationic Antimicrobial Peptides Bind with Their Hydrophobic Parts to Drug Site II of Human Serum Albumin. Authors: Sivertsen, A. / Isaksson, J. / Leiros, H.S. / Svenson, J. / Svendsen, J. / Brandsdal, B.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bke.cif.gz | 134.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bke.ent.gz | 102.7 KB | Display | PDB format |
PDBx/mmJSON format | 4bke.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bk/4bke ftp://data.pdbj.org/pub/pdb/validation_reports/bk/4bke | HTTPS FTP |
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-Related structure data
Related structure data | 1e7hS 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: 69469.695 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: BLOOD / Production host: SACCHAROMYCES CEREVISIAE (brewer's yeast) / References: UniProt: P02768 | ||
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#2: Chemical | ChemComp-PLM / #3: 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: 2.47 Å3/Da / Density % sol: 50.13 % / Description: NONE |
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Crystal grow | pH: 7.2 Details: 26 % PEG 3350, 50 MM KH2PO4 PH 7.2; 120 MG/ML IN 20 MM KH2PO4 AT PH 7.5 CONTAINING NOMINAL 0.1 MM PALMITIC ACID STREAK SEEDED SEEDING |
-Data collection
Diffraction | Mean temperature: 295 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: RIGAKU R-AXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→38.14 Å / Num. obs: 27926 / % possible obs: 96.5 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.3 |
Reflection shell | Resolution: 2.35→2.48 Å / Redundancy: 5 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.2 / % possible all: 95.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E7H Resolution: 2.35→20 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 8.942 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.379 / ESU R Free: 0.262 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.95 Å2
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Refinement step | Cycle: LAST / Resolution: 2.35→20 Å
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Refine LS restraints |
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