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- PDB-6xq8: Receptor for Advanced Glycation End Products VC1 domain in comple... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6xq8 | ||||||
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Title | Receptor for Advanced Glycation End Products VC1 domain in complex with Fragments 1 & 11 | ||||||
![]() | Advanced glycosylation end product-specific receptor | ||||||
![]() | SIGNALING PROTEIN / RAGE / IG-like domain / receptor / Advanced Glycation End Products | ||||||
Function / homology | ![]() regulation of CD4-positive, alpha-beta T cell activation / negative regulation of blood circulation / advanced glycation end-product receptor activity / positive regulation of endothelin production / regulation of T cell mediated cytotoxicity / glucose mediated signaling pathway / negative regulation of long-term synaptic depression / positive regulation of monocyte extravasation / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / positive regulation of dendritic cell differentiation ...regulation of CD4-positive, alpha-beta T cell activation / negative regulation of blood circulation / advanced glycation end-product receptor activity / positive regulation of endothelin production / regulation of T cell mediated cytotoxicity / glucose mediated signaling pathway / negative regulation of long-term synaptic depression / positive regulation of monocyte extravasation / positive regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process / positive regulation of dendritic cell differentiation / regulation of p38MAPK cascade / regulation of non-canonical NF-kappaB signal transduction / scavenger receptor activity / induction of positive chemotaxis / transcytosis / protein localization to membrane / positive regulation of monocyte chemotactic protein-1 production / positive regulation of heterotypic cell-cell adhesion / S100 protein binding / regulation of long-term synaptic potentiation / regulation of spontaneous synaptic transmission / laminin receptor activity / positive regulation of p38MAPK cascade / negative regulation of interleukin-10 production / positive regulation of activated T cell proliferation / response to amyloid-beta / TRAF6 mediated NF-kB activation / Advanced glycosylation endproduct receptor signaling / transport across blood-brain barrier / negative regulation of long-term synaptic potentiation / positive regulation of chemokine production / positive regulation of interleukin-12 production / astrocyte activation / positive regulation of interleukin-1 beta production / positive regulation of JNK cascade / microglial cell activation / TAK1-dependent IKK and NF-kappa-B activation / positive regulation of non-canonical NF-kappaB signal transduction / regulation of synaptic plasticity / transmembrane signaling receptor activity / fibrillar center / response to wounding / positive regulation of interleukin-6 production / cellular response to amyloid-beta / cell junction / positive regulation of tumor necrosis factor production / neuron projection development / regulation of inflammatory response / signaling receptor activity / positive regulation of NF-kappaB transcription factor activity / amyloid-beta binding / postsynapse / positive regulation of ERK1 and ERK2 cascade / learning or memory / cell surface receptor signaling pathway / molecular adaptor activity / response to hypoxia / positive regulation of protein phosphorylation / apical plasma membrane / inflammatory response / protein-containing complex binding / cell surface / extracellular region / identical protein binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Salay, L.E. / Kozlyuk, N. / Gilston, B.A. / Gogliotti, R.D. / Christov, P.P. / Kim, K. / Ovee, M. / Waterson, A.G. / Chazin, W.J. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A fragment-based approach to discovery of Receptor for Advanced Glycation End products inhibitors. Authors: Kozlyuk, N. / Gilston, B.A. / Salay, L.E. / Gogliotti, R.D. / Christov, P.P. / Kim, K. / Ovee, M. / Waterson, A.G. / Chazin, W.J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 198.8 KB | Display | ![]() |
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PDB format | ![]() | 140.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6xq1C ![]() 6xq3C ![]() 6xq5C ![]() 6xq6C ![]() 6xq7C ![]() 6xq9C ![]() 7lmlC ![]() 7lmwC ![]() 4lp4S C: citing same article ( 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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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
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Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 23131.494 Da / Num. of mol.: 2 / Fragment: VC1 domain, resdues 23-231 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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-Non-polymers , 5 types, 189 molecules ![](data/chem/img/ACT.gif)
![](data/chem/img/V6M.gif)
![](data/chem/img/V6P.gif)
![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/V6M.gif)
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![](data/chem/img/CL.gif)
![](data/chem/img/HOH.gif)
#2: Chemical | ChemComp-ACT / #3: Chemical | #4: Chemical | #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.34 Å3/Da / Density % sol: 63.14 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 2.5 M NaOAc (pH 7.5) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: RAYONIX MX-300 / Detector: CCD / Date: Feb 15, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97857 Å / Relative weight: 1 |
Reflection | Resolution: 1.82→50 Å / Num. obs: 107292 / % possible obs: 99.94 % / Redundancy: 4.2 % / Biso Wilson estimate: 24.37 Å2 / Rpim(I) all: 0.019 / Rrim(I) all: 0.056 / Net I/σ(I): 19.22 |
Reflection shell | Resolution: 1.82→1.89 Å / Redundancy: 4.2 % / Mean I/σ(I) obs: 5.05 / Num. unique obs: 10717 / Rpim(I) all: 0.107 / Rrim(I) all: 0.309 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4LP4 Resolution: 1.82→45.69 Å / SU ML: 0.1429 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 21.9303 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.91 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.82→45.69 Å
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Refine LS restraints |
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Refine LS restraints NCS | Type: Torsion NCS / Rms dev position: 0.458180071343 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
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