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Open data
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Basic information
Entry | Database: PDB / ID: 1aly | ||||||
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Title | CRYSTAL STRUCTURE OF HUMAN CD40 LIGAND | ||||||
![]() | CD40 LIGAND | ||||||
![]() | CYTOKINE / CD40L / CD40 LIGAND / TNF / HYPER-IGM SYNDROME | ||||||
Function / homology | ![]() CD40 receptor binding / CD40 signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of endothelial cell apoptotic process / isotype switching / tumor necrosis factor receptor binding / regulation of immunoglobulin production / leukocyte cell-cell adhesion / positive regulation of interleukin-4 production / B cell proliferation ...CD40 receptor binding / CD40 signaling pathway / TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway / positive regulation of endothelial cell apoptotic process / isotype switching / tumor necrosis factor receptor binding / regulation of immunoglobulin production / leukocyte cell-cell adhesion / positive regulation of interleukin-4 production / B cell proliferation / positive regulation of interleukin-10 production / positive regulation of T cell proliferation / T cell costimulation / positive regulation of interleukin-12 production / protein serine/threonine kinase activator activity / B cell differentiation / cytokine activity / TNFR2 non-canonical NF-kB pathway / integrin-mediated signaling pathway / platelet activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / integrin binding / positive regulation of NF-kappaB transcription factor activity / inflammatory response / external side of plasma membrane / negative regulation of apoptotic process / Golgi apparatus / cell surface / extracellular space / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Karpusas, M. / Hsu, Y.M. / Thomas, D. | ||||||
![]() | ![]() Title: 2 A crystal structure of an extracellular fragment of human CD40 ligand. Authors: Karpusas, M. / Hsu, Y.M. / Wang, J.H. / Thompson, J. / Lederman, S. / Chess, L. / Thomas, D. #1: ![]() Title: Erratum. 2 A Crystal Structure of an Extracellular Fragment of Human Cd40 Ligand Authors: Karpusas, M. / Hsu, Y.M. / Wang, J.H. / Thompson, J. / Lederman, S. / Chess, L. / Thomas, D. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 49.5 KB | Display | ![]() |
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PDB format | ![]() | 35.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 365.1 KB | Display | ![]() |
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Full document | ![]() | 373.4 KB | Display | |
Data in XML | ![]() | 5.5 KB | Display | |
Data in CIF | ![]() | 7.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1cdaS 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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1 | ![]()
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Unit cell |
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Details | THE ACTIVE MOLECULE IS A TRIMER GENERATED BY APPLYING THE THREE-FOLD SYMMETRY AROUND THE C AXIS. |
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Components
#1: Protein | Mass: 15812.817 Da / Num. of mol.: 1 / Fragment: EXTRACELLULAR DOMAIN FRAGMENT Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() |
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#2: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.97 Å3/Da / Density % sol: 62.46 % | ||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 7.5 Details: PROTEIN WAS CRYSTALLIZED FROM 1.4 M NA CITRATE, 50 MM HEPES PH 7.5 | ||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusionDetails: drop solution was mixed with an equal volume of reservoir solution | ||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 123 K |
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Diffraction source | Wavelength: 1.5418 |
Detector | Type: SIEMENS / Detector: AREA DETECTOR / Date: Jan 11, 1994 / Details: MIRRORS |
Radiation | Monochromator: GRAPHITE(002) / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.75→100 Å / Num. obs: 42587 / % possible obs: 77.1 % / Observed criterion σ(I): 2 / Redundancy: 2.71 % / Rmerge(I) obs: 0.067 / Rsym value: 0.056 / Net I/σ(I): 6.5 |
Reflection shell | Resolution: 1.75→1.84 Å / Redundancy: 1.2 % / Rmerge(I) obs: 0.056 / Mean I/σ(I) obs: 3.9 / Rsym value: 0.15 / % possible all: 46.1 |
Reflection | *PLUS Num. obs: 15693 / Num. measured all: 42587 |
Reflection shell | *PLUS % possible obs: 46.1 % |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1CDA Resolution: 2→7.5 Å / Rfactor Rfree error: 0.0002 / Data cutoff high absF: 10000000000 / Data cutoff low absF: 0.001 / Cross valid method: THROUGHOUT / σ(F): 2
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Refinement step | Cycle: LAST / Resolution: 2→7.5 Å
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Software | *PLUS Name: ![]() | ||||||||||||||||||||||||
Refinement | *PLUS | ||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||
Refine LS restraints | *PLUS
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