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Yorodumi- PDB-4uu9: Crystal structure of the human c5a in complex with MEDI7814 a neu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4uu9 | ||||||
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Title | Crystal structure of the human c5a in complex with MEDI7814 a neutralising antibody | ||||||
Components |
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Keywords | IMMUNE SYSTEM / FV / COMPLEMENT SYSTEM | ||||||
Function / homology | Function and homology information Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / positive regulation of chemokine production / Peptide ligand-binding receptors ...Terminal pathway of complement / membrane attack complex / Activation of C3 and C5 / negative regulation of macrophage chemotaxis / complement activation, alternative pathway / chemokine activity / endopeptidase inhibitor activity / positive regulation of vascular endothelial growth factor production / positive regulation of chemokine production / Peptide ligand-binding receptors / complement activation, classical pathway / Regulation of Complement cascade / chemotaxis / G alpha (i) signalling events / killing of cells of another organism / cell surface receptor signaling pathway / inflammatory response / G protein-coupled receptor signaling pathway / signaling receptor binding / extracellular space / extracellular exosome / extracellular region Similarity search - Function | ||||||
Biological species | HOMO SAPIENS (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å | ||||||
Authors | Colley, C. / Sridharan, S. / Dobson, C. / Popovic, B. / Debreczeni, J.E. / Hargreaves, D. / Edwards, B. / Brennan, J. / England, L. / Fung, S. ...Colley, C. / Sridharan, S. / Dobson, C. / Popovic, B. / Debreczeni, J.E. / Hargreaves, D. / Edwards, B. / Brennan, J. / England, L. / Fung, S. / An Eghobamien, L. / Sivars, U. / Woods, R. / Flavell, L. / Renshaw, G.J. / Wickson, K. / Wilkinson, T. / Davies, R. / Bonnell, J. / Warrener, P. / Howes, R. / Vaughan, T. | ||||||
Citation | Journal: MAbs / Year: 2018 Title: Structure and characterization of a high affinity C5a monoclonal antibody that blocks binding to C5aR1 and C5aR2 receptors. Authors: Colley, C.S. / Popovic, B. / Sridharan, S. / Debreczeni, J.E. / Hargeaves, D. / Fung, M. / An, L.L. / Edwards, B. / Arnold, J. / England, E. / Eghobamien, L. / Sivars, U. / Flavell, L. / ...Authors: Colley, C.S. / Popovic, B. / Sridharan, S. / Debreczeni, J.E. / Hargeaves, D. / Fung, M. / An, L.L. / Edwards, B. / Arnold, J. / England, E. / Eghobamien, L. / Sivars, U. / Flavell, L. / Renshaw, J. / Wickson, K. / Warrener, P. / Zha, J. / Bonnell, J. / Woods, R. / Wilkinson, T. / Dobson, C. / Vaughan, T.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4uu9.cif.gz | 233.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4uu9.ent.gz | 197.9 KB | Display | PDB format |
PDBx/mmJSON format | 4uu9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/uu/4uu9 ftp://data.pdbj.org/pub/pdb/validation_reports/uu/4uu9 | HTTPS FTP |
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-Related structure data
Similar structure data |
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-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
#1: Antibody | Mass: 13508.873 Da / Num. of mol.: 2 / Fragment: VARIABLE DOMAIN HEAVY CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: HUMANISED ANTIBODY FRAGMENT / Production host: ESCHERICHIA COLI BL21 (bacteria) #2: Antibody | Mass: 11629.880 Da / Num. of mol.: 2 / Fragment: VARIABLE DOMAIN LIGHT CHAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: HUMANISED ANTIBODY FRAGMENT / Production host: ESCHERICHIA COLI BL21 (bacteria) #3: Protein | Mass: 8375.754 Da / Num. of mol.: 2 / Fragment: C5A Source method: isolated from a genetically manipulated source Source: (gene. exp.) HOMO SAPIENS (human) / Description: HUMANISED ANTIBODY FRAGMENT / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: P01031 #4: Chemical | ChemComp-SO4 / #5: Water | ChemComp-HOH / | |
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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: 2.41 Å3/Da / Density % sol: 49 % / Description: NONE |
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Crystal grow | Details: 20% PEG10K, 8% ETHYLENE GLYCOL, 100MM HEPES PH 7.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Nov 13, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 2.12→126 Å / Num. obs: 48925 / % possible obs: 100 % / Observed criterion σ(I): 2 / Redundancy: 14.2 % / Rmerge(I) obs: 0.13 / Net I/σ(I): 19 |
Reflection shell | Resolution: 2.12→2.24 Å / Redundancy: 14.7 % / Rmerge(I) obs: 0.59 / Mean I/σ(I) obs: 8.4 / % possible all: 100 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.12→86.07 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.929 / SU B: 6.54 / SU ML: 0.09 / Cross valid method: THROUGHOUT / ESU R: 0.158 / ESU R Free: 0.14 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES WITH TLS ADDED
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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 mean: 28.421 Å2
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Refinement step | Cycle: LAST / Resolution: 2.12→86.07 Å
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