+Open data
-Basic information
Entry | Database: PDB / ID: 6tl7 | ||||||
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Title | CRYSTAL STRUCTURE OF LECTIN-LIKE OX-LDL RECEPTOR 1 (P212121) | ||||||
Components | Oxidized low-density lipoprotein receptor 1 | ||||||
Keywords | LIPID BINDING PROTEIN / LOX-1 / OLR1 / CTLD / C-TYPE LECTIN LIKE DOMAIN / SCAVENGER RECEPTOR / OXLDL BINDING | ||||||
Function / homology | Function and homology information 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 | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.11 Å | ||||||
Authors | Nar, H. / Fiegen, D. / Schnapp, G. | ||||||
Citation | Journal: Commun Chem / Year: 2020 Title: A small-molecule inhibitor of lectin-like oxidized LDL receptor-1 acts by stabilizing an inactive receptor tetramer state Authors: Nar, H. / Fiegen, D. / Schnapp, G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6tl7.cif.gz | 181.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6tl7.ent.gz | 119.8 KB | Display | PDB format |
PDBx/mmJSON format | 6tl7.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6tl7_validation.pdf.gz | 426.9 KB | Display | wwPDB validaton report |
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Full document | 6tl7_full_validation.pdf.gz | 427.3 KB | Display | |
Data in XML | 6tl7_validation.xml.gz | 18.3 KB | Display | |
Data in CIF | 6tl7_validation.cif.gz | 28.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/tl/6tl7 ftp://data.pdbj.org/pub/pdb/validation_reports/tl/6tl7 | HTTPS FTP |
-Related structure data
Related structure data | 6tl9C 6tlaC 1ypuS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15379.451 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: OLR1, CLEC8A, LOX1 / Production host: Escherichia coli (E. coli) / References: UniProt: P78380 #2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.18 Å3/Da / Density % sol: 43.49 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / Details: 30% PEG 2000MME, 0.15M KBr, pH 6.4-7.1 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 24, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.11→101.85 Å / Num. obs: 94380 / % possible obs: 88.8 % / Redundancy: 5.8 % / Biso Wilson estimate: 10.69 Å2 / Rmerge(I) obs: 0.05 / Rpim(I) all: 0.055 / Rrim(I) all: 0.055 / Net I/σ(I): 18.9 |
Reflection shell | Resolution: 1.11→1.17 Å / Rmerge(I) obs: 0.412 / Num. unique obs: 7658 / Rpim(I) all: 0.282 / Rrim(I) all: 0.505 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ypu Resolution: 1.11→34.32 Å / SU ML: 0.0776 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 15.3482 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: 16.35 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.11→34.32 Å
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Refine LS restraints |
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LS refinement shell |
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