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- PDB-5icx: Cetuximab Fab in complex with CQFDLSTRRLRCGGSK meditope -

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Basic information

Entry
Database: PDB / ID: 5icx
TitleCetuximab Fab in complex with CQFDLSTRRLRCGGSK meditope
Components
  • (Cetuximab Fab ...) x 2
  • Meditope
KeywordsIMMUNE SYSTEM / antibody / anti-EGFR
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBzymek, K.P. / Williams, J.C.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2016
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
DepositionFeb 23, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 15, 2016Provider: repository / Type: Initial release
Revision 1.1Dec 13, 2017Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.pdbx_database_id_PubMed ..._citation.journal_abbrev / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.2Jul 29, 2020Group: Data collection / Derived calculations / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_role
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.3Sep 27, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cetuximab Fab light chain
B: Cetuximab Fab heavy chain
C: Cetuximab Fab light chain
D: Cetuximab Fab heavy chain
E: Meditope
F: Meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)98,37411
Polymers97,7736
Non-polymers6015
Water6,143341
1
A: Cetuximab Fab light chain
B: Cetuximab Fab heavy chain
E: Meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,2986
Polymers48,8863
Non-polymers4113
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5820 Å2
ΔGint-40 kcal/mol
Surface area18720 Å2
MethodPISA
2
C: Cetuximab Fab light chain
D: Cetuximab Fab heavy chain
F: Meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,0765
Polymers48,8863
Non-polymers1902
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5430 Å2
ΔGint-44 kcal/mol
Surface area18500 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.220, 82.530, 212.530
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Antibody , 2 types, 4 molecules ACBD

#1: Antibody Cetuximab Fab light chain


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 Cetuximab Fab heavy chain


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

#3: Protein/peptide Meditope


Mass: 1873.168 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 2 types, 345 molecules

#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 341 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.12 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Dec 15, 2011
RadiationMonochromator: VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.8_1069refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GW1

4gw1


Resolution: 2.6→33 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 20.31
RfactorNum. reflection% reflection
Rfree0.222 1709 5 %
Rwork0.177 --
obs0.179 34159 95.9 %
Solvent computationShrinkage radii: 0.7 Å / VDW probe radii: 1.1 Å
Refinement stepCycle: LAST / Resolution: 2.6→33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6706 0 34 341 7081
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046942
X-RAY DIFFRACTIONf_angle_d0.7999452
X-RAY DIFFRACTIONf_dihedral_angle_d11.3652463
X-RAY DIFFRACTIONf_chiral_restr0.0531071
X-RAY DIFFRACTIONf_plane_restr0.0041209
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.67640.26071380.20162614X-RAY DIFFRACTION94
2.6764-2.76270.27161370.20122611X-RAY DIFFRACTION95
2.7627-2.86140.25861380.20452615X-RAY DIFFRACTION95
2.8614-2.97590.25631400.20122651X-RAY DIFFRACTION95
2.9759-3.11120.25321400.19522662X-RAY DIFFRACTION96
3.1112-3.27510.24571410.18342685X-RAY DIFFRACTION96
3.2751-3.48010.2481410.17672678X-RAY DIFFRACTION96
3.4801-3.74850.23351430.16032717X-RAY DIFFRACTION96
3.7485-4.1250.20011430.15182718X-RAY DIFFRACTION97
4.125-4.72050.15251450.1332747X-RAY DIFFRACTION97
4.7205-5.94160.18691480.16362810X-RAY DIFFRACTION97
5.9416-33.00230.22121550.22392942X-RAY DIFFRACTION97

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