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Yorodumi- PDB-6ktr: Crystal structure of fibroblast growth factor 19 in complex with Fab -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ktr | ||||||
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Title | Crystal structure of fibroblast growth factor 19 in complex with Fab | ||||||
Components |
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Keywords | IMMUNE SYSTEM/PROTEIN BINDING / complex / growth factor / antibody / CELL CYCLE / IMMUNE SYSTEM-PROTEIN BINDING complex | ||||||
Function / homology | Function and homology information negative regulation of bile acid biosynthetic process / betaKlotho-mediated ligand binding / fibroblast growth factor receptor binding / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / PI-3K cascade:FGFR4 / PI3K Cascade / fibroblast growth factor receptor signaling pathway / SHC-mediated cascade:FGFR4 / FRS-mediated FGFR4 signaling ...negative regulation of bile acid biosynthetic process / betaKlotho-mediated ligand binding / fibroblast growth factor receptor binding / FGFR4 ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / PI-3K cascade:FGFR4 / PI3K Cascade / fibroblast growth factor receptor signaling pathway / SHC-mediated cascade:FGFR4 / FRS-mediated FGFR4 signaling / regulation of cell migration / positive regulation of D-glucose import / animal organ morphogenesis / positive regulation of JNK cascade / Negative regulation of FGFR4 signaling / growth factor activity / Constitutive Signaling by Aberrant PI3K in Cancer / PIP3 activates AKT signaling / nervous system development / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / positive regulation of MAPK cascade / positive regulation of ERK1 and ERK2 cascade / cell differentiation / positive regulation of protein phosphorylation / negative regulation of gene expression / positive regulation of cell population proliferation / positive regulation of gene expression / extracellular space / extracellular region / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59775753879 Å | ||||||
Authors | Liu, H. / Zheng, S. / Hou, X. / Liu, X. / Lv, X. / Li, Y. / Li, W. / Sui, J. | ||||||
Funding support | China, 1items
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Citation | Journal: Cancer Sci. / Year: 2020 Title: Novel Abs targeting the N-terminus of fibroblast growth factor 19 inhibit hepatocellular carcinoma growth without bile-acid-related side-effects. Authors: Liu, H. / Zheng, S. / Hou, X. / Liu, X. / Du, K. / Lv, X. / Li, Y. / Yang, F. / Li, W. / Sui, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ktr.cif.gz | 288.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ktr.ent.gz | 185.2 KB | Display | PDB format |
PDBx/mmJSON format | 6ktr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ktr_validation.pdf.gz | 4.1 MB | Display | wwPDB validaton report |
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Full document | 6ktr_full_validation.pdf.gz | 4.1 MB | Display | |
Data in XML | 6ktr_validation.xml.gz | 43.2 KB | Display | |
Data in CIF | 6ktr_validation.cif.gz | 60 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kt/6ktr ftp://data.pdbj.org/pub/pdb/validation_reports/kt/6ktr | HTTPS FTP |
-Related structure data
Related structure data | 2p23S S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules CD
#3: Protein | Mass: 24556.787 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: FGF19, UNQ334/PRO533 / Production host: Homo sapiens (human) / References: UniProt: O95750 |
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-Antibody , 2 types, 4 molecules AFBG
#1: Antibody | Mass: 24876.699 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-F / Production host: Homo sapiens (human) #2: Antibody | Mass: 22715.943 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293-F / Production host: Homo sapiens (human) |
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-Non-polymers , 3 types, 278 molecules
#4: Chemical | ChemComp-SO4 / #5: Chemical | #6: Water | ChemComp-HOH / | |
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-Details
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: 2.53 Å3/Da / Density % sol: 51.47 % |
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Crystal grow | Temperature: 293.15 K / Method: vapor diffusion, hanging drop / pH: 6.9 Details: 0.2M Lithium Sulfate monohydrate, 0.1M Bis-Tris pH6.9, 26% w/v Polyethylene Glycol 3350 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.9793 Å |
Detector | Type: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Apr 16, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9793 Å / Relative weight: 1 |
Reflection | Resolution: 2.59→48.73 Å / Num. obs: 45911 / % possible obs: 99.7 % / Redundancy: 2 % / Biso Wilson estimate: 57.8977970902 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.017 / Rpim(I) all: 0.017 / Rsym value: 0.024 / Net I/σ(I): 3.3 |
Reflection shell | Resolution: 2.6→2.69 Å / Redundancy: 2 % / Rmerge(I) obs: 0.145 / Mean I/σ(I) obs: 3.3 / Num. unique obs: 4486 / CC1/2: 0.952 / Rpim(I) all: 0.145 / Rrim(I) all: 0.205 / % possible all: 99 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2P23 Resolution: 2.59775753879→48.7165078095 Å / SU ML: 0.415182139297 / Cross valid method: FREE R-VALUE / σ(F): 1.37685714956 / Phase error: 27.0492811013
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.8763097796 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.59775753879→48.7165078095 Å
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Refine LS restraints |
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LS refinement shell |
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