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- PDB-2aos: Protein-protein Interactions of protective signalling factor: Cry... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2aos | |||||||||
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Title | Protein-protein Interactions of protective signalling factor: Crystal structure of ternary complex involving signalling protein from goat (SPG-40), tetrasaccharide and a tripeptide Trp-pro-Trp at 2.9 A resolution | |||||||||
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![]() | SIGNALING PROTEIN / TERNARY COMPLEX / SIGNALLING PROTEIN / TETRASACCHARIDE / TRIPEPTIDE | |||||||||
Function / homology | ![]() response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / chitinase activity / chitin catabolic process / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-8 production ...response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / chitinase activity / chitin catabolic process / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-8 production / lung development / positive regulation of angiogenesis / cellular response to tumor necrosis factor / carbohydrate binding / carbohydrate metabolic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / inflammatory response / apoptotic process / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular space / cytoplasm Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() | |||||||||
![]() | Kumar, J. / Ethayathulla, A.S. / Srivastava, D.B. / Somvanshi, R.K. / Singh, N. / Sharma, S. / Dey, S. / Bhushan, A. / Kaur, P. / Singh, T.P. | |||||||||
![]() | ![]() Title: Protein-protein Interactions of protective signalling factor: Crystal structure of ternary complex involving signalling protein from goat (SPG-40), tetrasaccharide and a tripeptide Trp-pro-Trp at 2.9 A resolution Authors: Kumar, J. / Ethayathulla, A.S. / Srivastava, D.B. / Somvanshi, R.K. / Singh, N. / Sharma, S. / Dey, S. / Bhushan, A. / Kaur, P. / Singh, T.P. | |||||||||
History |
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Remark 999 | SEQUENCE According to authors, the sequence in the sequence database reference is incorrect for ...SEQUENCE According to authors, the sequence in the sequence database reference is incorrect for residues 54, 152, 226, 227, 274, 382 and residue 232 should be deleted from the sequence database reference. |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 92.6 KB | Display | ![]() |
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PDB format | ![]() | 69.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 522.5 KB | Display | ![]() |
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Full document | ![]() | 545.1 KB | Display | |
Data in XML | ![]() | 12.4 KB | Display | |
Data in CIF | ![]() | 18 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1ljyS ![]() 1zu6 ![]() 1zu7 ![]() 2aok 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
#1: Protein | Mass: 40728.090 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() |
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#2: Protein/peptide | Mass: 487.550 Da / Num. of mol.: 1 / Source method: obtained synthetically |
#3: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2- ...2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(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 | alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy- ...alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.8 Å3/Da / Density % sol: 56.3 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.8 Details: 25 mM TRIS-HCL, 50 mM NACL, 19% ETHANOL, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Aug 1, 2005 / Details: MIRROR |
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: 2.9→56 Å / Num. all: 10576 / Num. obs: 10278 / % possible obs: 96.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 50 Å2 / Rsym value: 0.11 / Net I/σ(I): 7.1 |
Reflection shell | Resolution: 2.9→3.12 Å / Mean I/σ(I) obs: 2 / Rsym value: 0.303 / % possible all: 98 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1LJY Resolution: 2.9→56 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.892 / SU B: 21.558 / SU ML: 0.414 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R Free: 0.399 / 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: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.236 Å2
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Refinement step | Cycle: LAST / Resolution: 2.9→56 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.901→2.976 Å / Total num. of bins used: 20 /
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