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Open data
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Basic information
Entry | Database: PDB / ID: 1kzd | ||||||
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Title | Complex of MBP-C and GlcNAc-terminated core | ||||||
![]() | MANNOSE-BINDING PROTEIN C | ||||||
![]() | IMMUNE SYSTEM / SUGAR BINDING PROTEIN / protein-carbohydrate complex | ||||||
Function / homology | ![]() Lectin pathway of complement activation / Initial triggering of complement / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / complement activation, lectin pathway / positive regulation of complement activation / galactose binding / negative regulation of viral process / positive regulation of protein processing / killing by host of symbiont cells ...Lectin pathway of complement activation / Initial triggering of complement / positive regulation of opsonization / cell surface pattern recognition receptor signaling pathway / complement activation, lectin pathway / positive regulation of complement activation / galactose binding / negative regulation of viral process / positive regulation of protein processing / killing by host of symbiont cells / collagen trimer / surfactant homeostasis / serine-type endopeptidase complex / phosphatidylinositol-4-phosphate binding / D-mannose binding / positive regulation of phagocytosis / antiviral innate immune response / multivesicular body / complement activation, classical pathway / calcium-dependent protein binding / protease binding / defense response to Gram-positive bacterium / innate immune response / signaling receptor binding / calcium ion binding / protein-containing complex / proteolysis / extracellular space / identical protein binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Ng, K.K. / Kolatkar, A.R. / Park-Snyder, S. / Feinberg, H. / Clark, D.A. / Drickamer, K. / Weis, W.I. | ||||||
![]() | ![]() Title: Orientation of bound ligands in mannose-binding proteins. Implications for multivalent ligand recognition. Authors: Ng, K.K. / Kolatkar, A.R. / Park-Snyder, S. / Feinberg, H. / Clark, D.A. / Drickamer, K. / Weis, W.I. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 65.3 KB | Display | ![]() |
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PDB format | ![]() | 46.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1kwtC ![]() 1kwuC ![]() 1kwvC ![]() 1kwwC ![]() 1kwxC ![]() 1kwyC ![]() 1kwzC ![]() 1kx0C ![]() 1kx1C ![]() 1kzaC ![]() 1kzbC ![]() 1kzcC ![]() 1kzeC ![]() 1rdoS 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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Details | non-physiological dimer |
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Components
#1: Protein | Mass: 12830.325 Da / Num. of mol.: 2 / Fragment: SUBTILISIN FRAGMENT (RESIDUES 129-243 of P08661) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Sugar | #3: Chemical | ChemComp-CA / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.62 % | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: PEG 8000, Tris-Cl, NaCl, CaCl2, NaN3, pH 7.4, VAPOR DIFFUSION, HANGING DROP at 298K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 20-22 ℃ / pH: 7.5 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Dec 12, 1994 |
Radiation | Monochromator: graphite / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→40 Å / Num. all: 20657 / Num. obs: 20657 / % possible obs: 97.4 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.183 / Rsym value: 0.183 / % possible all: 91.2 |
Reflection | *PLUS Lowest resolution: 40 Å |
Reflection shell | *PLUS % possible obs: 91.2 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1RDO Resolution: 1.9→40 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 1.9→40 Å
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Refine LS restraints |
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Refinement | *PLUS | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |