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- PDB-5hyq: Cetuximab Fab in complex with amidated meditope -

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Basic information

Entry
Database: PDB / ID: 5hyq
TitleCetuximab Fab in complex with amidated meditope
Components
  • Amidated meditope
  • Cetuximab heavy chain
  • Cetuximab light chain
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: 2.477 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 1, 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 1.2Sep 27, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cetuximab light chain
B: Cetuximab heavy chain
C: Cetuximab light chain
D: Cetuximab heavy chain
E: Amidated meditope
F: Amidated meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,4828
Polymers97,2926
Non-polymers1902
Water9,026501
1
A: Cetuximab light chain
B: Cetuximab heavy chain
E: Amidated meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7414
Polymers48,6463
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5780 Å2
ΔGint-43 kcal/mol
Surface area18460 Å2
MethodPISA
2
C: Cetuximab light chain
D: Cetuximab heavy chain
F: Amidated meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7414
Polymers48,6463
Non-polymers951
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5480 Å2
ΔGint-42 kcal/mol
Surface area18350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.130, 82.510, 212.230
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Antibody Cetuximab light chain


Mass: 23448.883 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 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)
#3: Protein/peptide Amidated meditope


Mass: 1471.771 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 501 / 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: 2.89 Å3/Da / Density % sol: 57.37 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.1 M citrate, 0.1 M sodium hydrogen phosphate, 0.5 M potassium hydrogen phosphate, 1.6 M sodium dihydrogen phosphate

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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: Jan 12, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.477→32.53 Å / Num. obs: 40620 / % possible obs: 99.1 % / Redundancy: 5.1 % / Rmerge(I) obs: 0.064 / Net I/σ(I): 22.9
Reflection shellResolution: 2.48→2.54 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.27 / % possible all: 88.9

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Processing

Software
NameVersionClassification
PHENIX(1.10_2155)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4gw1

4gw1


Resolution: 2.477→32.529 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 19.47
RfactorNum. reflection% reflection
Rfree0.2079 2031 5 %
Rwork0.1657 --
obs0.1678 40613 99.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.477→32.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6746 0 10 501 7257
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076950
X-RAY DIFFRACTIONf_angle_d0.8999480
X-RAY DIFFRACTIONf_dihedral_angle_d11.8294160
X-RAY DIFFRACTIONf_chiral_restr0.0521072
X-RAY DIFFRACTIONf_plane_restr0.0051213
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4774-2.5350.2931180.21332252X-RAY DIFFRACTION88
2.535-2.59840.24751350.19052558X-RAY DIFFRACTION100
2.5984-2.66860.21861340.17852560X-RAY DIFFRACTION100
2.6686-2.74710.23751350.18072552X-RAY DIFFRACTION100
2.7471-2.83570.24771340.18722550X-RAY DIFFRACTION100
2.8357-2.9370.24971350.19232562X-RAY DIFFRACTION100
2.937-3.05450.24541360.18322579X-RAY DIFFRACTION100
3.0545-3.19340.21281340.17162551X-RAY DIFFRACTION100
3.1934-3.36160.20341360.1662589X-RAY DIFFRACTION100
3.3616-3.5720.1881360.15682586X-RAY DIFFRACTION100
3.572-3.84740.18851360.14922578X-RAY DIFFRACTION100
3.8474-4.23390.16991370.14122608X-RAY DIFFRACTION100
4.2339-4.84480.16581380.12722622X-RAY DIFFRACTION100
4.8448-6.09730.21631400.15522654X-RAY DIFFRACTION100
6.0973-32.53140.20181470.20042781X-RAY DIFFRACTION99

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