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Open data
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Basic information
Entry | Database: PDB / ID: 5icx | ||||||
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Title | Cetuximab Fab in complex with CQFDLSTRRLRCGGSK meditope | ||||||
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![]() | IMMUNE SYSTEM / antibody / anti-EGFR | ||||||
Function / homology | Immunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION![]() | ||||||
Biological species | ![]() ![]() ![]() synthetic construct (others) | ||||||
Method | ![]() ![]() | ||||||
![]() | Bzymek, K.P. / Williams, J.C. | ||||||
![]() | ![]() Title: Cyclization strategies of meditopes: affinity and diffraction studies of meditope-Fab complexes. Authors: Bzymek, K.P. / Ma, Y. / Avery, K.A. / Horne, D.A. / Williams, J.C. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 187.9 KB | Display | ![]() |
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PDB format | ![]() | 147 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 5esqC ![]() 5hpmC ![]() 5hyqC ![]() 5icyC ![]() 5iczC ![]() 5id0C ![]() 5id1C ![]() 4gw1S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
-Antibody , 2 types, 4 molecules ACBD
#1: Antibody | Mass: 23287.705 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS, HOMO SAPIENS / Production host: unidentified (others) #2: Antibody | Mass: 23725.504 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS, HOMO SAPIENS / Production host: unidentified (others) |
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-Protein/peptide / Sugars , 2 types, 3 molecules EF![](data/chem/img/NAG.gif)
![](data/chem/img/NAG.gif)
#3: Protein/peptide | Mass: 1873.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #4: Sugar | ChemComp-NAG / | |
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-Non-polymers , 2 types, 345 molecules ![](data/chem/img/PO4.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/HOH.gif)
#5: Chemical | ChemComp-PO4 / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.12 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.1 M CITRIC ACID, 0.1 M SODIUM HYDROGEN PHOSPHATE, 0.4 M POTASSIUM HYDROGEN PHOSPHATE, 1.6 M SODIUM DIHYDROGEN PHOSPHATE, PH 5.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K PH range: 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 15, 2011 |
Radiation | Monochromator: VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.6→33 Å / Num. obs: 34163 / % possible obs: 95.8 % / Observed criterion σ(I): 2 / Redundancy: 4.35 % / Rmerge(I) obs: 0.082 / Net I/σ(I): 16.79 |
Reflection shell | Resolution: 2.6→2.67 Å / Redundancy: 4.36 % / Rmerge(I) obs: 0.338 / Mean I/σ(I) obs: 4.65 / % possible all: 93.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4GW1 Resolution: 2.6→33 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 20.31
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.6→33 Å
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Refine LS restraints |
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LS refinement shell |
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