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- PDB-4ayu: Structure of N-Acetyl-D-Proline bound to serum amyloid P component -
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Open data
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Basic information
Entry | Database: PDB / ID: 4ayu | ||||||
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Title | Structure of N-Acetyl-D-Proline bound to serum amyloid P component | ||||||
![]() | SERUM AMYLOID P-COMPONENT | ||||||
![]() | SUGAR BINDING PROTEIN / LECTIN | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Hughes, P. / Kolstoe, S.E. / Wood, S.P. | ||||||
![]() | ![]() 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: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 254.5 KB | Display | ![]() |
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PDB format | ![]() | 203.6 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 508.6 KB | Display | ![]() |
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Full document | ![]() | 519.3 KB | Display | |
Data in XML | ![]() | 54.8 KB | Display | |
Data in CIF | ![]() | 80.8 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4avsC ![]() 4avtC ![]() 4avvC ![]() 1sacS S: Starting model for refinement C: citing same article ( |
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Similar 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
-Protein / Sugars , 2 types, 10 molecules ABCDE![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#1: Protein | Mass: 23282.455 Da / Num. of mol.: 5 / Source method: isolated from a natural source / Source: (natural) ![]() #4: Sugar | ChemComp-NAG / |
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-Non-polymers , 4 types, 1382 molecules ![](data/chem/img/CA.gif)
![](data/chem/img/N8P.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/N8P.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-CA / #3: Chemical | ChemComp-N8P / #5: Chemical | ChemComp-GOL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 53 % / Description: NONE |
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Crystal grow | pH: 8 Details: 60 MM TRIS-HCL PH 8.0, 10 MM CACL2, 84 MM NACL, 20% GLYCEROL V/V, 17% PEG550 MME V/V |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 15, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→31.24 Å / Num. obs: 198644 / % possible obs: 96.5 % / Observed criterion σ(I): 2 / Redundancy: 7 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 14.1 |
Reflection shell | Resolution: 1.5→1.58 Å / Redundancy: 6.9 % / Rmerge(I) obs: 0.96 / Mean I/σ(I) obs: 2.6 / % possible all: 91 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1SAC Resolution: 1.5→28.663 Å / SU ML: 0.16 / σ(F): 1.34 / Phase error: 15.78 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.907 Å2 / ksol: 0.36 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.3 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→28.663 Å
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Refine LS restraints |
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LS refinement shell |
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