+Open data
-Basic information
Entry | Database: PDB / ID: 6m3c | ||||||
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Title | hAPC-h1573 Fab complex | ||||||
Components |
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Keywords | BLOOD CLOTTING/IMMUNE SYSTEM / human APC / h1573 Fab / complex / BLOOD CLOTTING / BLOOD CLOTTING-IMMUNE SYSTEM complex | ||||||
Function / homology | Function and homology information protein C (activated) / positive regulation of establishment of endothelial barrier / negative regulation of coagulation / negative regulation of blood coagulation / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / Post-translational protein phosphorylation ...protein C (activated) / positive regulation of establishment of endothelial barrier / negative regulation of coagulation / negative regulation of blood coagulation / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Common Pathway of Fibrin Clot Formation / Removal of aminoterminal propeptides from gamma-carboxylated proteins / Intrinsic Pathway of Fibrin Clot Formation / Post-translational protein phosphorylation / Cell surface interactions at the vascular wall / negative regulation of inflammatory response / Golgi lumen / Regulation of Insulin-like Growth Factor (IGF) transport and uptake by Insulin-like Growth Factor Binding Proteins (IGFBPs) / blood coagulation / endoplasmic reticulum lumen / serine-type endopeptidase activity / calcium ion binding / negative regulation of apoptotic process / Golgi apparatus / endoplasmic reticulum / proteolysis / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.7 Å | ||||||
Authors | Wang, X. / Wang, D. / Zhao, X. / Egner, U. | ||||||
Citation | Journal: Nat Commun / Year: 2020 Title: Targeted inhibition of activated protein C by a non-active-site inhibitory antibody to treat hemophilia. Authors: Zhao, X.Y. / Wilmen, A. / Wang, D. / Wang, X. / Bauzon, M. / Kim, J.Y. / Linden, L. / Li, L. / Egner, U. / Marquardt, T. / Moosmayer, D. / Tebbe, J. / Gluck, J.M. / Ellinger, P. / McLean, K. ...Authors: Zhao, X.Y. / Wilmen, A. / Wang, D. / Wang, X. / Bauzon, M. / Kim, J.Y. / Linden, L. / Li, L. / Egner, U. / Marquardt, T. / Moosmayer, D. / Tebbe, J. / Gluck, J.M. / Ellinger, P. / McLean, K. / Yuan, S. / Yegneswaran, S. / Jiang, X. / Evans, V. / Gu, J.M. / Schneider, D. / Zhu, Y. / Xu, Y. / Mallari, C. / Hesslein, A. / Wang, Y. / Schmidt, N. / Gutberlet, K. / Ruehl-Fehlert, C. / Freyberger, A. / Hermiston, T. / Patel, C. / Sim, D. / Mosnier, L.O. / Laux, V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6m3c.cif.gz | 855.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6m3c.ent.gz | 717.7 KB | Display | PDB format |
PDBx/mmJSON format | 6m3c.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/m3/6m3c ftp://data.pdbj.org/pub/pdb/validation_reports/m3/6m3c | HTTPS FTP |
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-Related structure data
Related structure data | 6m3bC 1autS 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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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS ensembles :
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-Components
#1: Protein | Mass: 28091.115 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PROC / Production host: Homo sapiens (human) / References: UniProt: P04070, protein C (activated) #2: Protein | Mass: 17607.980 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PROC / Production host: Homo sapiens (human) / References: UniProt: P04070, protein C (activated) #3: Antibody | Mass: 23749.223 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) #4: Antibody | Mass: 23779.533 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetulus griseus (Chinese hamster) |
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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: 4.6 Å3/Da / Density % sol: 73.28 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / Details: 0.2M sodium fluoride, 20% (w/v) PEG 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL17U1 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Oct 17, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.7→50 Å / Num. obs: 56425 / % possible obs: 98.42 % / Redundancy: 5.5 % / Biso Wilson estimate: 69.9 Å2 / Rpim(I) all: 0.149 / Net I/σ(I): 6.14 |
Reflection shell | Resolution: 3.7→3.79 Å / Num. unique obs: 3756 / CC1/2: 0.602 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1AUT Resolution: 3.7→33.385 Å / SU ML: 0.59 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 30 / Stereochemistry target values: ML
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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 max: 243.12 Å2 / Biso mean: 107.9789 Å2 / Biso min: 30 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 3.7→33.385 Å
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Refine LS restraints |
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Refine LS restraints NCS |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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