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- PDB-3imd: Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexib... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3imd | ||||||
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Title | Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexible Ac-pY-Q-N-NH2 Tripeptide Mimic | ||||||
![]() | Growth factor receptor-bound protein 2![]() | ||||||
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Function / homology | ![]() guanyl-nucleotide exchange factor adaptor activity / Grb2-EGFR complex / branching involved in labyrinthine layer morphogenesis / STAT5 Activation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Clements, J.H. | ||||||
![]() | ![]() Title: Thermodynamic and Structural Effects of Conformational Constraints in Protein-Ligand Interactions. Entropic Paradoxy Associated with Ligand Preorganization. Authors: Delorbe, J.E. / Clements, J.H. / Teresk, M.G. / Benfield, A.P. / Plake, H.R. / Millspaugh, L.E. / Martin, S.F. #1: ![]() Title: Ligand Preorganization May Be Accompanied by Entropic Penalties in Protein-Ligand Interactions Authors: Benfield, A.P. / Teresk, M.G. / Plake, H.R. / DeLorbe, J.E. / Millspaugh, L.E. / Martin, S.F. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 63 KB | Display | ![]() |
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PDB format | ![]() | 45 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3imjC ![]() 3in7C ![]() 3in8C ![]() 3kfjC ![]() 3c7iS 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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1 | ![]()
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2 | ![]()
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3 |
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Unit cell |
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Components
#1: Protein | ![]() Mass: 13758.543 Da / Num. of mol.: 2 / Fragment: SH2 domain Source method: isolated from a genetically manipulated source Details: Sequence was expressed with a C-terminal 6-his tag / Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() #2: Chemical | #3: Chemical | ChemComp-CL / ![]() #4: Chemical | ChemComp-MG / | #5: Water | ChemComp-HOH / | ![]() |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.789 Å3/Da / Density % sol: 31.262 % |
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Crystal grow![]() | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 Details: Ligand in lyphilized powder form was dissolved in a 9.1 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 2:1. 3 uL of this solution was mixed with 4 uL of 0.2 ...Details: Ligand in lyphilized powder form was dissolved in a 9.1 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 2:1. 3 uL of this solution was mixed with 4 uL of 0.2 M MgCl2 x 6H2O, 30% w/v PEG MW4000, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after four weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Mar 1, 2007 |
Radiation | Monochromator: blue max-flux confocal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.79→50 Å / Num. all: 19302 / Num. obs: 18279 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.9 % / Rmerge(I) obs: 0.049 / Χ2: 1.536 / Net I/σ(I): 50.8 |
Reflection shell | Resolution: 1.79→1.85 Å / Redundancy: 5.9 % / Rmerge(I) obs: 0.084 / Num. unique all: 1797 / Χ2: 1.85 / % possible all: 96.1 |
-Phasing
Phasing![]() | Method: ![]() |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: pdb entry 3C7I Resolution: 2→50 Å / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Solvent computation | Bsol: 11.411 Å2 | ||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 99.99 Å2 / Biso mean: 11.313 Å2 / Biso min: 1 Å2
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Refinement step | Cycle: LAST / Resolution: 2→50 Å
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Refine LS restraints |
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Xplor file |
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