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- PDB-6nfn: Fab fragment of anti-cocaine antibody h2E2 bound to benzoylecgonine -
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Open data
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Basic information
Entry | Database: PDB / ID: 6nfn | ||||||
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Title | Fab fragment of anti-cocaine antibody h2E2 bound to benzoylecgonine | ||||||
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![]() | IMMUNE SYSTEM / Fab-benzoylecgonine complex Fab fragment anti-cocaine antibody humanized mAb h2E2 | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / ACETATE ION / Chem-BCG / FORMIC ACID / DI(HYDROXYETHYL)ETHER![]() | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Pokkuluri, P.R. / Tan, K. | ||||||
![]() | ![]() Title: Structural analysis of free and liganded forms of the Fab fragment of a high-affinity anti-cocaine antibody, h2E2. Authors: Tan, K. / Zhou, M. / Ahrendt, A.J. / Duke, N.E.C. / Tabaja, N. / Ball, W.J. / Kirley, T.L. / Norman, A.B. / Joachimiak, A. / Schiffer, M. / Wilton, R. / Pokkuluri, P.R. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1.3 MB | Display | ![]() |
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PDB format | ![]() | 1 MB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 6nexC ![]() 3t2nS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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8 | ![]()
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Unit cell |
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Components
-Antibody , 2 types, 16 molecules LACEIOQMHBDFJPRN
#1: Antibody | Mass: 22768.576 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() #2: Antibody | Mass: 23720.492 Da / Num. of mol.: 8 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() ![]() |
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-Non-polymers , 6 types, 193 molecules ![](data/chem/img/BCG.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/PEG.gif)
![](data/chem/img/GOL.gif)
![](data/chem/img/ACT.gif)
![](data/chem/img/FMT.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | ChemComp-BCG / #4: Chemical | ChemComp-PEG / | #5: Chemical | ChemComp-GOL / | #6: Chemical | ChemComp-ACT / #7: Chemical | ChemComp-FMT / | #8: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | Y |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.63 Å3/Da / Density % sol: 53.16 % |
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Crystal grow | Temperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: G10 of PEG/Ion HT (2% Tascimate pH 7.0, 0.1 M HEPES pH 7.5, 20% PEG3350) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 10, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97915 Å / Relative weight: 1 |
Reflection | Resolution: 2.63→50 Å / Num. obs: 104134 / % possible obs: 99 % / Observed criterion σ(I): -3 / Redundancy: 3.5 % / Biso Wilson estimate: 46.63 Å2 / CC1/2: 0.983 / Rmerge(I) obs: 0.119 / Rpim(I) all: 0.074 / Rrim(I) all: 0.14 / Χ2: 1.405 / Net I/σ(I): 13.9 |
Reflection shell | Resolution: 2.63→2.68 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.805 / Mean I/σ(I) obs: 1.61 / Num. unique obs: 5217 / CC1/2: 0.572 / Rpim(I) all: 0.537 / Rrim(I) all: 0.97 / Χ2: 0.881 / % possible all: 98.5 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3T2N Resolution: 2.63→38.67 Å / SU ML: 0.3452 / Cross valid method: FREE R-VALUE / σ(F): 1.97 / Phase error: 27.689 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
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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 mean: 61.54 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.63→38.67 Å
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Refine LS restraints |
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LS refinement shell |
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