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- PDB-1beh: HUMAN PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN IN COMPLEX WITH CA... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1beh | ||||||
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Title | HUMAN PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN IN COMPLEX WITH CACODYLATE | ||||||
![]() | PHOSPHATIDYLETHANOLAMINE BINDING PROTEIN | ||||||
![]() | LIPID BINDING PROTEIN / LIPID-BINDING / SIGNALLING | ||||||
Function / homology | ![]() phosphatidylethanolamine binding / negative regulation of MAPK cascade / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / serine-type endopeptidase inhibitor activity / Negative regulation of MAPK pathway / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions ...phosphatidylethanolamine binding / negative regulation of MAPK cascade / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / serine-type endopeptidase inhibitor activity / Negative regulation of MAPK pathway / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / Signaling by BRAF and RAF1 fusions / protein kinase binding / enzyme binding / RNA binding / extracellular exosome / ATP binding / nucleus / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Banfield, M.J. / Barker, J.J. / Perry, A. / Brady, R.L. | ||||||
![]() | ![]() Title: Function from structure? The crystal structure of human phosphatidylethanolamine-binding protein suggests a role in membrane signal transduction. Authors: Banfield, M.J. / Barker, J.J. / Perry, A.C. / Brady, R.L. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 88.1 KB | Display | ![]() |
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PDB format | ![]() | 67.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 445.6 KB | Display | ![]() |
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Full document | ![]() | 450.4 KB | Display | |
Data in XML | ![]() | 18.3 KB | Display | |
Data in CIF | ![]() | 26.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1bd9SC 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper: (Code: given Matrix: (0.48316, 0.87203, -0.07827), Vector: |
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Components
#1: Protein | Mass: 21086.787 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.2 Å3/Da / Density % sol: 36 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.5 Details: PROTEIN WAS CRYSTALLIZED FROM 28-32% PEG 4000/6000/8000, 200-300 MM SODIUM ACETATE, 100MM SODIUM CACODYLATE., pH 6.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: unknown | ||||||||||||||||||||||||||||||||||||||||||||||||
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: MARRESEARCH / Detector: IMAGE PLATE / Date: Apr 15, 1997 / Details: MIRRORS |
Radiation | Monochromator: GE(111) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.7→20 Å / Num. obs: 38803 / % possible obs: 95.6 % / Observed criterion σ(I): -3 / Redundancy: 2.4 % / Biso Wilson estimate: 19.1 Å2 / Rmerge(I) obs: 0.055 / Net I/σ(I): 16.2 |
Reflection shell | Resolution: 1.7→1.76 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.6 / % possible all: 94.9 |
Reflection shell | *PLUS % possible obs: 94.9 % |
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Processing
Software |
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1BD9 Resolution: 1.75→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
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Displacement parameters | Biso mean: 24 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.75→20 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Rfactor obs: 0.235 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | *PLUS Highest resolution: 1.75 Å / Lowest resolution: 1.83 Å / Rfactor all: 0.268 / Rfactor obs: 0.322 |