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Yorodumi- PDB-7lmp: Structure of full-length human lambda-6A light chain JTO in compl... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7lmp | |||||||||
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Title | Structure of full-length human lambda-6A light chain JTO in complex with stabilizer 36 [3-(2-(7-(diethylamino)-4-methyl-2-oxo-2H-chromen-3-yl)ethyl)-8-(1H-imidazole-4-carbonyl)-1,3,8-triazaspiro[4.5]decane-2,4-dione] | |||||||||
Components | JTO light chain | |||||||||
Keywords | IMMUNE SYSTEM / amyloidosis | |||||||||
Function / homology | Chem-NY6 / PHOSPHATE ION Function and homology information | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 Å | |||||||||
Authors | Yan, N.L. / Wilson, I.A. / Kelly, J.W. | |||||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2021 Title: Discovery of Potent Coumarin-Based Kinetic Stabilizers of Amyloidogenic Immunoglobulin Light Chains Using Structure-Based Design. Authors: Yan, N.L. / Santos-Martins, D. / Nair, R. / Chu, A. / Wilson, I.A. / Johnson, K.A. / Forli, S. / Morgan, G.J. / Petrassi, H.M. / Kelly, J.W. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7lmp.cif.gz | 104.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7lmp.ent.gz | 77 KB | Display | PDB format |
PDBx/mmJSON format | 7lmp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7lmp_validation.pdf.gz | 741.1 KB | Display | wwPDB validaton report |
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Full document | 7lmp_full_validation.pdf.gz | 741.9 KB | Display | |
Data in XML | 7lmp_validation.xml.gz | 19.5 KB | Display | |
Data in CIF | 7lmp_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lm/7lmp ftp://data.pdbj.org/pub/pdb/validation_reports/lm/7lmp | HTTPS FTP |
-Related structure data
Related structure data | 7lmnC 7lmoC 7lmqC 7lmrC 6mg5S 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: Antibody | Mass: 23211.543 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #2: Chemical | #3: Chemical | ChemComp-NY6 / | #4: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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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: 2.69 Å3/Da / Density % sol: 54.24 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, sitting drop / Details: 20% PEG 3350 and 0.25 M NH4H2PO4 at 23 degrees C |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 23-ID-B / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Nov 26, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 2.29→47.54 Å / Num. obs: 23063 / % possible obs: 99.9 % / Redundancy: 13.3 % / Biso Wilson estimate: 25 Å2 / CC1/2: 1 / Rpim(I) all: 0.037 / Rsym value: 0.13 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.29→2.42 Å / Redundancy: 13.6 % / Mean I/σ(I) obs: 2.3 / Num. unique obs: 3282 / CC1/2: 0.82 / Rpim(I) all: 0.298 / Rsym value: 1.008 / % possible all: 99.1 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6MG5 Resolution: 2.29→47.54 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.909 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.328 / ESU R Free: 0.25 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 129.15 Å2 / Biso mean: 36.568 Å2 / Biso min: 19.78 Å2
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Refinement step | Cycle: final / Resolution: 2.29→47.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.294→2.354 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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