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Open data
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Basic information
Entry | Database: PDB / ID: 6wmh | ||||||
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Title | Next generation monomeric IgG4 Fc | ||||||
![]() | Immunoglobulin heavy constant gamma 4 | ||||||
![]() | IMMUNE SYSTEM / antibody constant region / fragment crystallizable / mutated | ||||||
Function / homology | ![]() IgG immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Regulation of Complement cascade ...IgG immunoglobulin complex / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / Role of phospholipids in phagocytosis / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCGR3A-mediated IL10 synthesis / complement activation, classical pathway / Regulation of Complement cascade / FCGR3A-mediated phagocytosis / antigen binding / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / antibacterial humoral response / Interleukin-4 and Interleukin-13 signaling / adaptive immune response / blood microparticle / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Oganesyan, V.Y. / Shan, L. / van Dyk, N. / Dall'Acqua, W.F. | ||||||
![]() | ![]() Title: In vivo pharmacokinetic enhancement of monomeric Fc and monovalent bispecific designs through structural guidance. Authors: Shan, L. / Dyk, N.V. / Haskins, N. / Cook, K.M. / Rosenthal, K.L. / Mazor, R. / Dragulin-Otto, S. / Jiang, Y. / Wu, H. / Dall'Acqua, W.F. / Borrok, M.J. / Damschroder, M.M. / Oganesyan, V. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 100.5 KB | Display | ![]() |
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PDB format | ![]() | 75.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.2 KB | Display | ![]() |
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Full document | ![]() | 436.3 KB | Display | |
Data in XML | ![]() | 18 KB | Display | |
Data in CIF | ![]() | 25.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6wibC ![]() 6wnaC ![]() 6wolC ![]() 5hvwS S: Starting model for refinement C: citing same article ( |
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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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2 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: PRO / Beg label comp-ID: PRO / End auth comp-ID: SER / End label comp-ID: SER / Refine code: _ / Auth seq-ID: 238 - 442 / Label seq-ID: 1 - 205
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Components
#1: Protein | Mass: 23789.652 Da / Num. of mol.: 2 / Fragment: domains Ch2 and Ch3 Mutation: M252Y, S254T, T256E, N297D, L351F, S354E, T366R, P395K, F405R, Y407E Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 52 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 7.5 Details: DL-Glutamic acid monohydrate, DL-Alanine, Glycine, DL-Lysine monohydrochloride, DL-Serine, Sodium HEPES, MOPS (acid), Ethylene glycol, PEG 8000 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: May 12, 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: 2.3→37 Å / Num. obs: 22417 / % possible obs: 99.2 % / Redundancy: 6.8 % / CC1/2: 0.987 / Rmerge(I) obs: 0.169 / Rpim(I) all: 0.069 / Net I/σ(I): 7.4 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 6.7 % / Rmerge(I) obs: 1.282 / Num. unique obs: 2147 / CC1/2: 0.599 / Rpim(I) all: 0.528 / % possible all: 98.2 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5hvw Resolution: 2.3→35 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.926 / SU B: 8.019 / SU ML: 0.186 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.324 / ESU R Free: 0.231 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 201.11 Å2 / Biso mean: 44.781 Å2 / Biso min: 21.44 Å2
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Refinement step | Cycle: final / Resolution: 2.3→35 Å
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Refine LS restraints |
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Refine LS restraints NCS | Ens-ID: 1 / Number: 5799 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.13 Å / Weight position: 0.05
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LS refinement shell | Resolution: 2.3→2.357 Å / Rfactor Rfree error: 0
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