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- PDB-5id1: Cetuximab Fab in complex with MPT-Cys meditope -

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Basic information

Entry
Database: PDB / ID: 5id1
TitleCetuximab Fab in complex with MPT-Cys 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: 2.49 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)97,54311
Polymers96,9426
Non-polymers6015
Water7,548419
1
A: Cetuximab Fab light chain
B: Cetuximab Fab heavy chain
F: Meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8826
Polymers48,4713
Non-polymers4113
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5730 Å2
ΔGint-38 kcal/mol
Surface area18620 Å2
MethodPISA
2
C: Cetuximab Fab light chain
D: Cetuximab Fab heavy chain
E: Meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6615
Polymers48,4713
Non-polymers1902
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5380 Å2
ΔGint-43 kcal/mol
Surface area18490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.160, 83.160, 212.580
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: 1457.742 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 / N-Acetylglucosamine


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, 423 molecules

#5: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 419 / 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: 2.93 Å3/Da / Density % sol: 57.95 %
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: Apr 12, 2012
RadiationMonochromator: VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.49→34.43 Å / Num. obs: 40643 / % possible obs: 99.2 % / Observed criterion σ(I): 2 / Redundancy: 7.8 % / Rmerge(I) obs: 0.042 / Net I/σ(I): 39.42
Reflection shellResolution: 2.49→2.55 Å / Redundancy: 5.7 % / Rmerge(I) obs: 0.138 / Mean I/σ(I) obs: 11 / % possible all: 92.5

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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: 2.49→34.43 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 20.87
RfactorNum. reflection% reflection
Rfree0.221 2033 5 %
Rwork0.173 --
obs0.175 40633 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Refinement stepCycle: LAST / Resolution: 2.49→34.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6679 0 34 419 7132
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086891
X-RAY DIFFRACTIONf_angle_d1.1919374
X-RAY DIFFRACTIONf_dihedral_angle_d13.6812445
X-RAY DIFFRACTIONf_chiral_restr0.0751061
X-RAY DIFFRACTIONf_plane_restr0.0051197
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.49-2.54370.29061250.19692361X-RAY DIFFRACTION92
2.5437-2.60730.29231310.19572494X-RAY DIFFRACTION98
2.6073-2.67780.28691360.19412576X-RAY DIFFRACTION100
2.6778-2.75660.25881340.20142546X-RAY DIFFRACTION100
2.7566-2.84550.26541330.20172542X-RAY DIFFRACTION100
2.8455-2.94710.25911340.20122545X-RAY DIFFRACTION100
2.9471-3.06510.23631370.20422607X-RAY DIFFRACTION100
3.0651-3.20450.26991350.19362562X-RAY DIFFRACTION100
3.2045-3.37330.27361360.17792577X-RAY DIFFRACTION100
3.3733-3.58440.211350.17142565X-RAY DIFFRACTION100
3.5844-3.86080.21441350.16392575X-RAY DIFFRACTION100
3.8608-4.24870.1761380.1452604X-RAY DIFFRACTION100
4.2487-4.86210.15091370.12722616X-RAY DIFFRACTION100
4.8621-6.12010.17831400.14982650X-RAY DIFFRACTION100
6.1201-34.43580.20661470.19332780X-RAY DIFFRACTION99

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