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- PDB-1uj3: Crystal structure of a humanized Fab fragment of anti-tissue-fact... -
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Open data
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Basic information
Entry | Database: PDB / ID: 1uj3 | ||||||
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Title | Crystal structure of a humanized Fab fragment of anti-tissue-factor antibody in complex with tissue factor | ||||||
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Function / homology | ![]() activation of plasma proteins involved in acute inflammatory response / activation of blood coagulation via clotting cascade / serine-type peptidase complex / positive regulation of platelet-derived growth factor receptor signaling pathway / NGF-stimulated transcription / positive regulation of positive chemotaxis / Extrinsic Pathway of Fibrin Clot Formation / ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Ohto, U. / Mizutani, R. / Nakamura, M. / Adachi, H. / Satow, Y. | ||||||
![]() | ![]() Title: Crystal structure of a humanized Fab fragment of anti-tissue-factor antibody in complex with tissue factor. Authors: Ohto, U. / Mizutani, R. / Nakamura, M. / Adachi, H. / Satow, Y. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 147 KB | Display | ![]() |
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PDB format | ![]() | 112.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Antibody | Mass: 23475.979 Da / Num. of mol.: 1 / Fragment: anti-tissue-factor antibody hATR-5 Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
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#2: Antibody | Mass: 23255.990 Da / Num. of mol.: 1 / Fragment: anti-tissue-factor antibody hATR-5 Fab Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
#3: Protein | ![]() Mass: 23302.949 Da / Num. of mol.: 1 / Fragment: RESIDUES 606-810 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() ![]() |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 3.85 Å3/Da / Density % sol: 67.77 % |
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Crystal grow![]() | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 2-propanol, PEG4000, HEPES-Na, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 5, 2002 |
Radiation | Monochromator: SI 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→37.1 Å / Num. all: 69013 / Num. obs: 64872 / % possible obs: 94 % / Observed criterion σ(F): 3 / Biso Wilson estimate: 19.2 Å2 / Rmerge(I) obs: 0.087 |
Reflection shell | Resolution: 2.1→2.2 Å / % possible all: 81 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRIES 2HFT AND 1JPT Resolution: 2.1→37.01 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1947766.14 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 3 / Stereochemistry target values: Engh & Huber
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Solvent computation | Solvent model: FLAT MODEL / Bsol: 44.9528 Å2 / ksol: 0.339345 e/Å3 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 32.3 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.1→37.01 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.23 Å / Rfactor Rfree error: 0.008 / Total num. of bins used: 6
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Xplor file |
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