+Open data
-Basic information
Entry | Database: PDB / ID: 4avv | |||||||||
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Title | Structure of CPHPC bound to Serum Amyloid P Component | |||||||||
Components | SERUM AMYLOID P-COMPONENTSerum amyloid P component | |||||||||
Keywords | SUGAR BINDING PROTEIN / LECTIN / METAL-BINDING | |||||||||
Function / homology | Function and homology information negative regulation by host of viral exo-alpha-sialidase activity / negative regulation by host of viral glycoprotein metabolic process / negative regulation of exo-alpha-sialidase activity / negative regulation of glycoprotein metabolic process / complement component C1q complex binding / negative regulation of viral process / negative regulation of wound healing / negative regulation of monocyte differentiation / negative regulation of viral entry into host cell / virion binding ...negative regulation by host of viral exo-alpha-sialidase activity / negative regulation by host of viral glycoprotein metabolic process / negative regulation of exo-alpha-sialidase activity / negative regulation of glycoprotein metabolic process / complement component C1q complex binding / negative regulation of viral process / negative regulation of wound healing / negative regulation of monocyte differentiation / negative regulation of viral entry into host cell / virion binding / negative regulation of acute inflammatory response / chaperone-mediated protein complex assembly / acute-phase response / unfolded protein binding / protein folding / carbohydrate binding / collagen-containing extracellular matrix / blood microparticle / Amyloid fiber formation / innate immune response / calcium ion binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / nucleus Similarity search - Function | |||||||||
Biological species | HOMO SAPIENS (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | |||||||||
Authors | Kolstoe, S.E. / Jenvey, M.C. / Wood, S.P. | |||||||||
Citation | Journal: Acta Crystallogr.,Sect.D / Year: 2014 Title: Interaction of Serum Amyloid P Component with Hexanoyl Bis(D-Proline) (Cphpc) Authors: Kolstoe, S.E. / Jenvey, M.C. / Purvis, A. / Light, M.E. / Thompson, D. / Hughes, P. / Pepys, M.B. / Wood, S.P. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4avv.cif.gz | 273.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4avv.ent.gz | 218.2 KB | Display | PDB format |
PDBx/mmJSON format | 4avv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/av/4avv ftp://data.pdbj.org/pub/pdb/validation_reports/av/4avv | HTTPS FTP |
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-Related structure data
Related structure data | 4avsC 4avtC 4ayuC 1sacS 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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Unit cell |
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Components on special symmetry positions |
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-Components
-Protein , 1 types, 5 molecules ABCDE
#1: Protein | Mass: 23282.455 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) HOMO SAPIENS (human) / References: UniProt: P02743 |
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-Sugars , 4 types, 6 molecules
#2: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
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#3: Polysaccharide | N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D- ...N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source | ||
#7: Sugar | #8: Sugar | ChemComp-SIA / | |
-Non-polymers , 4 types, 1449 molecules
#4: Chemical | ChemComp-ACT / #5: Chemical | ChemComp-GHE / ( #6: Chemical | ChemComp-CD / #9: 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: 2.67 Å3/Da / Density % sol: 54 % / Description: NONE |
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Crystal grow | pH: 4.6 / Details: PH 4.6 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.98 |
Detector | Type: ADSC QUANTUM 210 / Detector: CCD |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→1.69 Å / Num. obs: 170912 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 12.4 |
Reflection shell | Resolution: 1.6→1.69 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.21 / Mean I/σ(I) obs: 3.5 / % possible all: 98.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1SAC Resolution: 1.6→37.869 Å / SU ML: 0.09 / σ(F): 1.35 / Phase error: 15.44 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.73 Å / VDW probe radii: 1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 59.961 Å2 / ksol: 0.4 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.9 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→37.869 Å
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Refine LS restraints |
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LS refinement shell |
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