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Open data
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Basic information
Entry | Database: PDB / ID: 2i6s | |||||||||
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Title | Complement component C2a | |||||||||
![]() | Complement C2a fragment | |||||||||
![]() | HYDROLASE / Serine protease domain / von Willebrand Factor-A domain | |||||||||
Function / homology | ![]() classical-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / positive regulation of apoptotic cell clearance / response to thyroid hormone / Activation of C3 and C5 / complement activation / Initial triggering of complement / response to nutrient / complement activation, classical pathway / Regulation of Complement cascade ...classical-complement-pathway C3/C5 convertase / classical-complement-pathway C3/C5 convertase complex / positive regulation of apoptotic cell clearance / response to thyroid hormone / Activation of C3 and C5 / complement activation / Initial triggering of complement / response to nutrient / complement activation, classical pathway / Regulation of Complement cascade / response to bacterium / response to lipopolysaccharide / serine-type endopeptidase activity / innate immune response / proteolysis / extracellular space / extracellular exosome / extracellular region / metal ion binding Similarity search - Function | |||||||||
Biological species | ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Milder, F.J. / Raaijmakers, H.C.A. / Vandeputte, D.A.A. / Schouten, A. / Huizinga, E.G. / Romijn, R.A. / Hemrika, W. / Roos, A. / Daha, M.R. / Gros, P. | |||||||||
![]() | ![]() Title: Structure of complement component c2a: implications for convertase formation and substrate binding. Authors: Milder, F.J. / Raaijmakers, H.C. / Vandeputte, M.D. / Schouten, A. / Huizinga, E.G. / Romijn, R.A. / Hemrika, W. / Roos, A. / Daha, M.R. / Gros, 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 | ![]() | 116.7 KB | Display | ![]() |
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PDB format | ![]() | 88.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.3 MB | Display | ![]() |
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Full document | ![]() | 1.3 MB | Display | |
Data in XML | ![]() | 20.7 KB | Display | |
Data in CIF | ![]() | 27.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2i6qC ![]() 1dleS ![]() 1q0pS C: citing same article ( S: Starting model for refinement |
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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 / Non-polymers , 2 types, 39 molecules A![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#1: Protein | Mass: 58464.484 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() References: UniProt: P06681, classical-complement-pathway C3/C5 convertase |
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#6: Water | ChemComp-HOH / |
-Sugars , 4 types, 5 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6) ...beta-D-mannopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[beta-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#3: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...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 |
#4: 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 |
#5: Sugar |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 44.18 % |
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Crystal grow | Temperature: 293 K / Method: hanging drop vapor diffusion / pH: 7 Details: 35% PEG 1000, 0.025 M sodium malonate, 0.0375 M imidazole, 0.0375 M boric acid, 20 mM LiCl, pH 7.0, hanging drop vapor diffusion, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 18, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9393 Å / Relative weight: 1 |
Reflection | Resolution: 2.7→37.54 Å / Num. obs: 13881 / % possible obs: 98.5 % / Redundancy: 3.6 % / Rmerge(I) obs: 0.085 / Rsym value: 0.085 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.7→2.85 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 1.8 / Num. measured all: 5710 / Num. unique all: 1850 / Rsym value: 0.42 / % possible all: 90.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB Entries: 1DLE (SP-domain) and 1Q0P (VWA-domain) Resolution: 2.7→37.5 Å / Cor.coef. Fo:Fc: 0.934 / Cor.coef. Fo:Fc free: 0.853 / SU B: 35.401 / SU ML: 0.357 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.442 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.118 Å2
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Refinement step | Cycle: LAST / Resolution: 2.7→37.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.7→2.77 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION / Selection: ALL / Auth asym-ID: A / Label asym-ID: A
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