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Yorodumi- PDB-8cn9: Factor VII binding Fab of the bispecific antibody HMB-001 in comp... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8cn9 | ||||||
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Title | Factor VII binding Fab of the bispecific antibody HMB-001 in complex with Factor VII | ||||||
Components |
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Keywords | BLOOD CLOTTING / Factor VII / Fab / Bispecific Antibody / HMB-001 | ||||||
Function / homology | Function and homology information activation of blood coagulation via clotting cascade / activation of plasma proteins involved in acute inflammatory response / coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway ...activation of blood coagulation via clotting cascade / activation of plasma proteins involved in acute inflammatory response / coagulation factor VIIa / response to Thyroid stimulating hormone / response to 2,3,7,8-tetrachlorodibenzodioxine / response to astaxanthin / response to thyrotropin-releasing hormone / response to genistein / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / response to vitamin K / response to carbon dioxide / response to thyroxine / NGF-stimulated transcription / response to cholesterol / response to growth hormone / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / positive regulation of leukocyte chemotaxis / cytokine receptor activity / positive regulation of TOR signaling / positive regulation of blood coagulation / animal organ regeneration / Gamma-carboxylation of protein precursors / Transport of gamma-carboxylated protein precursors from the endoplasmic reticulum to the Golgi apparatus / Removal of aminoterminal propeptides from gamma-carboxylated proteins / positive regulation of endothelial cell proliferation / serine-type peptidase activity / BMAL1:CLOCK,NPAS2 activates circadian gene expression / positive regulation of interleukin-8 production / protein processing / phospholipid binding / cytokine-mediated signaling pathway / Golgi lumen / circadian rhythm / response to estrogen / positive regulation of angiogenesis / activation of cysteine-type endopeptidase activity involved in apoptotic process / blood coagulation / response to estradiol / collagen-containing extracellular matrix / protease binding / vesicle / response to hypoxia / positive regulation of cell migration / endoplasmic reticulum lumen / external side of plasma membrane / serine-type endopeptidase activity / signaling receptor binding / calcium ion binding / positive regulation of gene expression / cell surface / extracellular space / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Schluckebier, G. / Johansson, E. | ||||||
Funding support | 1items
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Citation | Journal: Nat Cardiovasc Res / Year: 2023 Title: A bispecific antibody approach for the potential prophylactic treatment of inherited bleeding disorders Authors: Gandhi, P.S. / Zivkovic, M. / Oestergaard, H. / Bonde, A.C. / Loevgreen, M.N. / Schluckebier, G. / Johansson, E. / Rea, C.J. / Soerensen, B. / Schutgens, R.E. / Urbanus, R.T. / Faber, J.H. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8cn9.cif.gz | 916.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8cn9.ent.gz | 602.1 KB | Display | PDB format |
PDBx/mmJSON format | 8cn9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 8cn9_validation.pdf.gz | 615.5 KB | Display | wwPDB validaton report |
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Full document | 8cn9_full_validation.pdf.gz | 666.5 KB | Display | |
Data in XML | 8cn9_validation.xml.gz | 126.5 KB | Display | |
Data in CIF | 8cn9_validation.cif.gz | 169.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/cn/8cn9 ftp://data.pdbj.org/pub/pdb/validation_reports/cn/8cn9 | HTTPS FTP |
-Related structure data
Related structure data | 8cheC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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-Components
-Coagulation factor ... , 2 types, 8 molecules CHMRDINS
#3: Protein | Mass: 28103.256 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Production host: Homo sapiens (human) / References: UniProt: P08709, coagulation factor VIIa #4: Protein | Mass: 11670.991 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F7 / Production host: Homo sapiens (human) / References: UniProt: P08709, coagulation factor VIIa |
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-Antibody , 2 types, 8 molecules AFKPBGLQ
#1: Antibody | Mass: 23384.982 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) #2: Antibody | Mass: 23434.117 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human) |
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-Protein / Sugars , 2 types, 7 molecules EJOT
#5: Protein | Mass: 24826.512 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: F3 / Production host: Homo sapiens (human) / References: UniProt: P13726 #7: Sugar | |
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-Non-polymers , 2 types, 11 molecules
#6: Chemical | ChemComp-CA / #8: Chemical | ChemComp-CS / | |
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-Details
Has ligand of interest | N |
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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: 2.92 Å3/Da / Density % sol: 57.86 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.3 Details: 0.15 M Cesium chloride 15% w/v Polyethylene glycol 3,350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU FR-X / Wavelength: 1.5418 Å |
Detector | Type: DECTRIS PILATUS3 R 1M / Detector: PIXEL / Date: May 8, 2018 / Details: na |
Radiation | Monochromator: Mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→48.5 Å / Num. obs: 69059 / % possible obs: 96.3 % / Redundancy: 4.9 % / Biso Wilson estimate: 63.86 Å2 / CC1/2: 0.98 / CC star: 0.995 / Rmerge(I) obs: 0.31 / Rpim(I) all: 0.15 / Rrim(I) all: 0.35 / Net I/σ(I): 3.6 |
Reflection shell | Resolution: 3.4→3.522 Å / Redundancy: 3.7 % / Rmerge(I) obs: 1.05 / Mean I/σ(I) obs: 0.86 / Num. unique obs: 6423 / CC1/2: 0.697 / CC star: 0.906 / Rrim(I) all: 1.21 / % possible all: 91.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.4→48.5 Å / SU ML: 0.6377 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 41.0162 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 64.3 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 3.4→48.5 Å
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Refine LS restraints |
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LS refinement shell |
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