+Open data
-Basic information
Entry | Database: PDB / ID: 3bn9 | ||||||
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Title | Crystal Structure of MT-SP1 in complex with Fab Inhibitor E2 | ||||||
Components |
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Keywords | HYDROLASE / Antibody-Protease Complex / Protein-Protein Complex / Enzyme-Inhibitor Complex / Disease mutation / Glycoprotein / Membrane / Polymorphism / Serine protease / Signal-anchor / Transmembrane | ||||||
Function / homology | Function and homology information matriptase / epithelial cell morphogenesis involved in placental branching / acrosome reaction / Formation of the cornified envelope / CD22 mediated BCR regulation / immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation ...matriptase / epithelial cell morphogenesis involved in placental branching / acrosome reaction / Formation of the cornified envelope / CD22 mediated BCR regulation / immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / Classical antibody-mediated complement activation / Initial triggering of complement / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / keratinocyte differentiation / serine-type peptidase activity / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / neural tube closure / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / antigen binding / protein catabolic process / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / basolateral plasma membrane / Potential therapeutics for SARS / blood microparticle / immune response / external side of plasma membrane / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular exosome / extracellular region / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.173 Å | ||||||
Authors | Farady, C.J. / Schneider, E.L. / Egea, P.F. / Goetz, D.H. / Craik, C.S. | ||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: Structure of an Fab-protease complex reveals a highly specific non-canonical mechanism of inhibition Authors: Farady, C.J. / Egea, P.F. / Schneider, E.L. / Darragh, M.R. / Craik, C.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3bn9.cif.gz | 536.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3bn9.ent.gz | 439.7 KB | Display | PDB format |
PDBx/mmJSON format | 3bn9.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3bn9_validation.pdf.gz | 512.3 KB | Display | wwPDB validaton report |
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Full document | 3bn9_full_validation.pdf.gz | 564.4 KB | Display | |
Data in XML | 3bn9_validation.xml.gz | 64.8 KB | Display | |
Data in CIF | 3bn9_validation.cif.gz | 91 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bn/3bn9 ftp://data.pdbj.org/pub/pdb/validation_reports/bn/3bn9 | HTTPS FTP |
-Related structure data
Related structure data | 1eaxS 2hffS 3bn5 S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules BA
#1: Protein | Mass: 26447.689 Da / Num. of mol.: 2 / Fragment: Peptidase S1 domain / Mutation: C122S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ST14, PRSS14, SNC19, TADG15 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9Y5Y6, matriptase |
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-Antibody , 2 types, 4 molecules CEDF
#2: Antibody | Mass: 23245.787 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) #3: Antibody | Mass: 27131.283 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P01764*PLUS |
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-Non-polymers , 3 types, 839 molecules
#4: Chemical | ChemComp-EDO / #5: Chemical | #6: 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: 2.72 Å3/Da / Density % sol: 54.78 % |
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Crystal grow | Temperature: 293 K / pH: 8 Details: 16% PEG 5000 MME, 0.21M AmSO4, 0.1M Tris, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 12, 2007 / Details: KOHZU DOUBLE CRYSTAL SI (111) |
Radiation | Monochromator: KOHZU DOUBLE CRYSTAL SI (111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.173→85.64 Å / Num. obs: 74972 / % possible obs: 89.4 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Biso Wilson estimate: 29.4 Å2 / Rmerge(I) obs: 0.091 / Net I/σ(I): 7.5 |
Reflection shell | Resolution: 2.173→2.3 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.569 / Mean I/σ(I) obs: 1.7 / % possible all: 77.4 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1EAX, 2HFF Resolution: 2.173→85.64 Å / SU ML: 0.34 / σ(F): 1.35 / Phase error: 31.57 / 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 / Bsol: 46.62 Å2 / ksol: 0.34 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.28 Å2
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Refinement step | Cycle: LAST / Resolution: 2.173→85.64 Å
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Refine LS restraints |
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LS refinement shell |
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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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