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Yorodumi- PDB-3k2u: Crystal structure of HGFA in complex with the allosteric inhibito... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3k2u | |||||||||
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Title | Crystal structure of HGFA in complex with the allosteric inhibitory antibody Fab40 | |||||||||
Components |
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Keywords | HYDROLASE/IMMUNE SYSTEM / Serine Protease / Allosteric inhibitor / Antibody / EGF-like domain / GLYCOPROTEIN / Fab complex / HYDROLASE / Disulfide bond / Kringle / Protease / Secreted / Zymogen / HYDROLASE-IMMUNE SYSTEM complex | |||||||||
Function / homology | Function and homology information MET Receptor Activation / zymogen activation / Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases / rough endoplasmic reticulum / serine-type peptidase activity / blood coagulation / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / cytosol Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.35 Å | |||||||||
Authors | Ganesan, R. / Eigenbrot, C. / Shia, S. | |||||||||
Citation | Journal: Structure / Year: 2009 Title: Unraveling the allosteric mechanism of serine protease inhibition by an antibody. Authors: Ganesan, R. / Eigenbrot, C. / Wu, Y. / Liang, W.C. / Shia, S. / Lipari, M.T. / Kirchhofer, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3k2u.cif.gz | 146.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3k2u.ent.gz | 110.9 KB | Display | PDB format |
PDBx/mmJSON format | 3k2u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/k2/3k2u ftp://data.pdbj.org/pub/pdb/validation_reports/k2/3k2u | HTTPS FTP |
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-Related structure data
Related structure data | 2wubC 2wucC 2r0lS 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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1 |
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Unit cell |
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-Components
-Hepatocyte growth factor activator ... , 2 types, 2 molecules AB
#1: Protein | Mass: 27982.635 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia Ni (cabbage looper) References: UniProt: Q04756, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
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#2: Protein/peptide | Mass: 3962.654 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Trichoplusia Ni (cabbage looper) References: UniProt: Q04756, Hydrolases; Acting on peptide bonds (peptidases); Serine endopeptidases |
-Antibody , 2 types, 2 molecules HL
#3: Antibody | Mass: 23770.605 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): 33D3 |
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#4: Antibody | Mass: 23238.748 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / Strain (production host): 33D3 |
-Sugars / Non-polymers , 2 types, 169 molecules
#5: Polysaccharide | 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#6: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.21 Å3/Da / Density % sol: 44.34 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 14% PEG 10,000, 100 mM HEPES pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.97946 Å |
Detector | Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Nov 20, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97946 Å / Relative weight: 1 |
Reflection | Resolution: 2.35→50 Å / Num. all: 61952 / Num. obs: 30979 / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 2 % / Biso Wilson estimate: 37.7 Å2 / Rsym value: 0.05 / Net I/σ(I): 15 |
Reflection shell | Resolution: 2.35→2.43 Å / Redundancy: 1.9 % / Mean I/σ(I) obs: 2.9 / Rsym value: 0.198 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2R0L Resolution: 2.35→19.77 Å / Rfactor Rfree error: 0.006 / Data cutoff high absF: 894977.79 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 50.9654 Å2 / ksol: 0.35 e/Å3 | ||||||||||||||||||||
Displacement parameters | Biso mean: 66.6 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.35→19.77 Å
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Refine LS restraints |
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Refine LS restraints NCS | NCS model details: NONE | ||||||||||||||||||||
LS refinement shell | Resolution: 2.35→2.5 Å / Rfactor Rfree error: 0.021 / Total num. of bins used: 6
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Xplor file |
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