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- PDB-7r8u: LOX-1 - Structural and Functional Studies of a Receptor Implicate... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7r8u | ||||||
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Title | LOX-1 - Structural and Functional Studies of a Receptor Implicated in Atherosclerosis | ||||||
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![]() | SIGNALING PROTEIN/IMMUNE SYSTEM / Low Density Lipoprotein Receptor Antibody complex LOX-1 Scavenger receptor Atherogenesis-Atherosclerosis Macrophage Cardiovascular disease / SIGNALING PROTEIN-IMMUNE SYSTEM complex | ||||||
Function / homology | ![]() low-density lipoprotein particle receptor activity / lipoprotein metabolic process / blood circulation / leukocyte cell-cell adhesion / immune system process / tertiary granule membrane / specific granule membrane / Cell surface interactions at the vascular wall / carbohydrate binding / receptor complex ...low-density lipoprotein particle receptor activity / lipoprotein metabolic process / blood circulation / leukocyte cell-cell adhesion / immune system process / tertiary granule membrane / specific granule membrane / Cell surface interactions at the vascular wall / carbohydrate binding / receptor complex / inflammatory response / membrane raft / intracellular membrane-bounded organelle / Neutrophil degranulation / proteolysis / extracellular region / nucleoplasm / identical protein binding / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oganesyan, V. / van Dyk, N. | ||||||
![]() | ![]() Title: Structural and functional studies of a monoclonal antibody blocking LOX-1 Authors: Ongstad, E.L. / Gaddipati, R. / Belkhodja, M. / van Dyk, N. / Levy, S. / Sagar, D. / Cariuk, P. / Wolny, M. / Hanna, R.N. / Borrok, M.J. / Buchanan, A. / Oganesyan, V. / Gupta, R. | ||||||
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 169.1 KB | Display | ![]() |
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PDB format | ![]() | Display | ![]() | |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 1ypuS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 15028.069 Da / Num. of mol.: 2 / Fragment: Extracellular fragment (UNP residues 140-271) Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Antibody | | Mass: 24764.836 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Antibody | | Mass: 22700.006 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.33 Å3/Da / Density % sol: 47.1 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion Details: 0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M 1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol, 1 M Tris base, BICINE, pH 8.5, 50% v/v precipitant mix (25% v/v ...Details: 0.2 M 1,6-hexanediol, 0.2 M 1-butanol, 0.2 M 1,2-propanediol, 0.2 M 2-propanol, 0.2 M 1,4-butanediol, 0.2 M 1,3-propanediol, 1 M Tris base, BICINE, pH 8.5, 50% v/v precipitant mix (25% v/v MPD, 25% PEG1000, 25% w/v PEG3350) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jan 28, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.19499 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→39.492 Å / Num. obs: 57364 / % possible obs: 96.9 % / Redundancy: 6.5 % / CC1/2: 0.995 / Net I/σ(I): 1.6 |
Reflection shell | Resolution: 1.9→1.94 Å / Num. unique obs: 3538 / CC1/2: 0.65 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 1YPU Resolution: 1.901→39.492 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.957 / SU B: 4.399 / SU ML: 0.12 / Cross valid method: THROUGHOUT / ESU R: 0.155 / ESU R Free: 0.137 Details: Hydrogens have been added in their riding positions
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.913 Å2
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Refinement step | Cycle: LAST / Resolution: 1.901→39.492 Å
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Refine LS restraints |
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LS refinement shell |
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