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- PDB-5etu: Cetuximab Fab in complex with L5E meditope variant -

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Basic information

Entry
Database: PDB / ID: 5etu
TitleCetuximab Fab in complex with L5E meditope variant
Components
  • Cetuximab Fab heavy chain
  • Cetuximab Fab light chain
  • L5E meditope variant
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: 2.53 Å
AuthorsBzymek, K.P. / Williams, J.C.
CitationJournal: Acta Crystallogr F Struct Biol Commun / Year: 2016
Title: Natural and non-natural amino-acid side-chain substitutions: affinity and diffraction studies of meditope-Fab complexes.
Authors: Bzymek, K.P. / Avery, K.A. / Ma, Y. / Horne, D.A. / Williams, J.C.
History
DepositionNov 18, 2015Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Dec 13, 2017Group: Database references / Derived calculations / Category: citation / pdbx_struct_oper_list
Item: _citation.journal_abbrev / _citation.page_first ..._citation.journal_abbrev / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Sep 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

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: L5E meditope variant
F: L5E meditope variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,30511
Polymers96,8306
Non-polymers4755
Water7,008389
1
A: Cetuximab Fab light chain
B: Cetuximab Fab heavy chain
E: L5E meditope variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6055
Polymers48,4153
Non-polymers1902
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5400 Å2
ΔGint-37 kcal/mol
Surface area18930 Å2
MethodPISA
2
C: Cetuximab Fab light chain
D: Cetuximab Fab heavy chain
F: L5E meditope variant
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7006
Polymers48,4153
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5490 Å2
ΔGint-40 kcal/mol
Surface area18810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.380, 82.870, 213.000
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 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: 23638.426 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 L5E meditope variant


Mass: 1488.712 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#4: Chemical
ChemComp-PO4 / PHOSPHATE ION / Phosphate


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


Mass: 18.015 Da / Num. of mol.: 389 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.08 %
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

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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: Nov 23, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.53→32.65 Å / Num. obs: 38822 / % possible obs: 99.6 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.129 / Net I/σ(I): 23.5
Reflection shellResolution: 2.53→2.6 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.637 / Mean I/σ(I) obs: 7.3 / % possible all: 98.1

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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: 2.53→32.65 Å / SU ML: 0.32 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 21.82 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2322 1942 5 %
Rwork0.1804 --
obs0.183 38822 99.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.53→32.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6712 0 25 389 7126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0036939
X-RAY DIFFRACTIONf_angle_d0.6839472
X-RAY DIFFRACTIONf_dihedral_angle_d11.2184150
X-RAY DIFFRACTIONf_chiral_restr0.0461068
X-RAY DIFFRACTIONf_plane_restr0.0041212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5299-2.59320.34741350.26442565X-RAY DIFFRACTION98
2.5932-2.66320.28841360.232589X-RAY DIFFRACTION100
2.6632-2.74160.28611360.2262584X-RAY DIFFRACTION100
2.7416-2.830.31911380.23042609X-RAY DIFFRACTION100
2.83-2.93110.27621370.21742616X-RAY DIFFRACTION100
2.9311-3.04840.28571370.20552603X-RAY DIFFRACTION100
3.0484-3.1870.24841380.19372622X-RAY DIFFRACTION100
3.187-3.35490.22311370.18432598X-RAY DIFFRACTION100
3.3549-3.56480.22381390.16992634X-RAY DIFFRACTION100
3.5648-3.83970.21341380.16072627X-RAY DIFFRACTION100
3.8397-4.22530.21261390.14732647X-RAY DIFFRACTION100
4.2253-4.83510.17441400.13392665X-RAY DIFFRACTION100
4.8351-6.08520.20591420.15792696X-RAY DIFFRACTION100
6.0852-32.65530.1991500.19082825X-RAY DIFFRACTION99

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