+Open data
-Basic information
Entry | Database: PDB / ID: 2bx8 | |||||||||
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Title | Human serum albumin complexed with azapropazone | |||||||||
Components | SERUM ALBUMIN | |||||||||
Keywords | TRANSPORT PROTEIN / ALBUMIN / CARRIER PROTEIN / LIPID-BINDING / FATTY ACID / METAL- BINDING / DRUG-BINDING / AZAPROPAZONE / TRANSPORT | |||||||||
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å | |||||||||
Authors | Ghuman, J. / Zunszain, P.A. / Petitpas, I. / Bhattacharya, A.A. / Curry, S. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2005 Title: Structural Basis of the Drug-Binding Specificity of Human Serum Albumin. Authors: Ghuman, J. / Zunszain, P.A. / Petitpas, I. / Bhattacharya, A.A. / Otagiri, M. / Curry, S. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2bx8.cif.gz | 227.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2bx8.ent.gz | 180.4 KB | Display | PDB format |
PDBx/mmJSON format | 2bx8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bx/2bx8 ftp://data.pdbj.org/pub/pdb/validation_reports/bx/2bx8 | HTTPS FTP |
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-Related structure data
Related structure data | 2bxaC 2bxbC 2bxcC 2bxdC 2bxeC 2bxfC 2bxgC 2bxhC 2bxiC 2bxkC 2bxlC 2bxmC 2bxnC 2bxoC 2bxpC 2bxqC 1e78S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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 oper: (Code: given Matrix: (0.4369, 0.8991, 0.0258), Vector: |
-Components
#1: Protein | Mass: 66571.219 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Tissue: PLASMA / Production host: PICHIA PASTORIS (fungus) / References: UniProt: P02768 #2: Chemical | ChemComp-AZQ / Sequence details | SEQUENCE IS FOR PRE-CURSOR. MATURE POLYPEPTIDE WAS CRYSTALLISED (WHICH LACKS SIGNAL AND PROPEPTIDES ...SEQUENCE IS FOR PRE-CURSOR. MATURE POLYPEPTID | |
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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: 2.39 Å3/Da / Density % sol: 42 % |
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Crystal grow | pH: 7 / Details: pH 7.00 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.81 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 15, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→41.5 Å / Num. obs: 32332 / % possible obs: 95.6 % / Observed criterion σ(I): 0 / Redundancy: 2 % / Biso Wilson estimate: 54.1 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 2 % / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 2.9 / % possible all: 95.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1E78 Resolution: 2.7→41.45 Å / Rfactor Rfree error: 0.007 / Data cutoff high absF: 1038934.58 / Isotropic thermal model: GROUP / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MLF Details: AZP AND AZQ IN THE TOPOLOGY THE DRUG AZAPROPAZONE BUT REFER TO THE DIFFERENT PUCKERS OF THE FUSED RING SYSTEM. AZQ.TOP AND AZQ.PAR WERE USED FOR A2001, WHILE AZP.TOP AND AZP.PAR WERE USED FOR A2002
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 52.304 Å2 / ksol: 0.277814 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 77.9 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.7→41.45 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.87 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6
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Xplor file |
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