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- PDB-5l5c: Plexin A1 full extracellular region, domains 1 to 10, to 6 angstr... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5l5c | |||||||||
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Title | Plexin A1 full extracellular region, domains 1 to 10, to 6 angstrom, spacegroup P4(3)2(1)2 | |||||||||
![]() | Plexin-A1 | |||||||||
![]() | SIGNALING PROTEIN / receptor / signaling / axon guidance | |||||||||
Function / homology | ![]() olfactory nerve formation / Other semaphorin interactions / CRMPs in Sema3A signaling / RHOD GTPase cycle / Sema3A PAK dependent Axon repulsion / neuron projection guidance / dichotomous subdivision of terminal units involved in salivary gland branching / RND1 GTPase cycle / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion ...olfactory nerve formation / Other semaphorin interactions / CRMPs in Sema3A signaling / RHOD GTPase cycle / Sema3A PAK dependent Axon repulsion / neuron projection guidance / dichotomous subdivision of terminal units involved in salivary gland branching / RND1 GTPase cycle / gonadotrophin-releasing hormone neuronal migration to the hypothalamus / SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion / semaphorin-plexin signaling pathway involved in axon guidance / semaphorin receptor activity / negative regulation of cell adhesion / regulation of smooth muscle cell migration / semaphorin receptor complex / neuron projection extension / positive regulation of axonogenesis / regulation of cell migration / regulation of cell shape / nucleoplasm / membrane / plasma membrane / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Janssen, B.J.C. / Kong, Y. / Malinauskas, T. / Vangoor, V.R. / Coles, C.H. / Kaufmann, R. / Ni, T. / Gilbert, R.J.C. / Padilla-Parra, S. / Pasterkamp, R.J. / Jones, E.Y. | |||||||||
![]() | ![]() Title: Structural Basis for Plexin Activation and Regulation. Authors: Kong, Y. / Janssen, B.J. / Malinauskas, T. / Vangoor, V.R. / Coles, C.H. / Kaufmann, R. / Ni, T. / Gilbert, R.J. / Padilla-Parra, S. / Pasterkamp, R.J. / Jones, E.Y. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 229.3 KB | Display | ![]() |
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PDB format | ![]() | 172.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 2 MB | Display | ![]() |
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Full document | ![]() | 2 MB | Display | |
Data in XML | ![]() | 30.5 KB | Display | |
Data in CIF | ![]() | 44.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5l56SC ![]() 5l59C ![]() 5l5gC ![]() 5l5kC ![]() 5l5lC ![]() 5l5mC ![]() 5l5nC ![]() 5l74C ![]() 5l7nC 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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Unit cell |
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Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 134024.828 Da / Num. of mol.: 1 / Fragment: UNP residues 37-1236 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Sugars , 6 types, 10 molecules ![](data/chem/img/NAG.gif)
#2: Polysaccharide | Source method: isolated from a genetically manipulated source #3: Polysaccharide | Source method: isolated from a genetically manipulated source #4: Polysaccharide | Source method: isolated from a genetically manipulated source #5: 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 #6: 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 #7: Sugar | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density % sol: 82 % |
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Crystal grow | Temperature: 293.5 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 6% (w/v) PEG 4k, 5 mM tricine, pH 8.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M-F / Detector: PIXEL / Date: May 29, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9173 Å / Relative weight: 1 |
Reflection | Resolution: 6→119.503 Å / Num. obs: 11641 / % possible obs: 98.8 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.71 / Net I/σ(I): 9.7 |
Reflection shell | Highest resolution: 6 Å / Rmerge(I) obs: 1.24 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5L56 Resolution: 6→119.503 Å / SU ML: 1.1 / Cross valid method: FREE R-VALUE / σ(F): 1.15 / Phase error: 38.29 Details: THE AUTHORS STATE THAT DUE TO THE LOW RESOLUTION OF THE DIFFRACTION DATA THE STRUCTURE WAS ONLY SUBJECTED TO RIGID BODY REFINEMENT WITH EACH DOMAIN AS RIGID BODY. THE STRUCTURE IS BASED ON ...Details: THE AUTHORS STATE THAT DUE TO THE LOW RESOLUTION OF THE DIFFRACTION DATA THE STRUCTURE WAS ONLY SUBJECTED TO RIGID BODY REFINEMENT WITH EACH DOMAIN AS RIGID BODY. THE STRUCTURE IS BASED ON PDB ENTRY 5L56. THE AUTHORS HAVE NOT FURTHER REFINED THE RESULTING COORDINATES NOR CORRECTED RESULTING CLASHES BETWEEN ATOMS AND DEVIATING PEPTIDE LINKAGES BETWEEN DOMAINS.
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 6→119.503 Å
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Refine LS restraints |
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LS refinement shell |
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