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- PDB-5euk: Cetuximab Fab in complex with F3H meditope variant -

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Basic information

Entry
Database: PDB / ID: 5euk
TitleCetuximab Fab in complex with F3H meditope variant
Components
  • (Cetuximab Fab ...) x 2
  • F3H meditope
KeywordsIMMUNE SYSTEM / antibody / anti-EGFR
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / MESO-ERYTHRITOL / PHOSPHATE ION
Function and homology information
Biological speciesMUS MUSCULUS (house mouse)
HOMO SAPIENS (human)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.5 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 1.3Jul 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 1.4Sep 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
Revision 1.5Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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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: F3H meditope
F: F3H meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,72413
Polymers96,7806
Non-polymers9447
Water7,386410
1
A: Cetuximab Fab light chain
B: Cetuximab Fab heavy chain
E: F3H meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8967
Polymers48,3903
Non-polymers5064
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6190 Å2
ΔGint-43 kcal/mol
Surface area18550 Å2
MethodPISA
2
C: Cetuximab Fab light chain
D: Cetuximab Fab heavy chain
F: F3H meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8286
Polymers48,3903
Non-polymers4383
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5760 Å2
ΔGint-28 kcal/mol
Surface area18570 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.930, 82.060, 212.090
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: 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)

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Protein/peptide / Sugars , 2 types, 4 molecules EF

#3: Protein/peptide F3H meditope


Mass: 1463.729 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#5: 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.: 2
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 , 3 types, 415 molecules

#4: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: PO4
#6: Chemical ChemComp-MRY / MESO-ERYTHRITOL


Mass: 122.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O4
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 410 / Source method: isolated from a natural source / Formula: H2O

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Details

Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.87 Å3/Da / Density % sol: 57.2 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.3
Details: 0.1 M citric acid, 0.1 M sodium phosphate dibasic, 0.4 M potassium phosphate dibasic, 1.6 M sodium phosphate monobasic

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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: Oct 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→32.83 Å / Num. obs: 39428 / % possible obs: 99.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.126 / Net I/σ(I): 11.3
Reflection shellResolution: 2.5→2.56 Å / Redundancy: 3 % / Rmerge(I) obs: 0.775 / Mean I/σ(I) obs: 1.8 / % possible all: 92.9

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Processing

Software
NameVersionClassification
PHENIXdev_1426refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4GW1

4gw1


Resolution: 2.5→32.83 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 23.27 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2337 1971 5 %
Rwork0.1714 --
obs0.1746 39421 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.5→32.83 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6744 0 56 410 7210
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0086987
X-RAY DIFFRACTIONf_angle_d1.1939507
X-RAY DIFFRACTIONf_dihedral_angle_d13.4552492
X-RAY DIFFRACTIONf_chiral_restr0.0781080
X-RAY DIFFRACTIONf_plane_restr0.0051212
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.495-2.55740.36861300.25672476X-RAY DIFFRACTION93
2.5574-2.62650.29691380.22152611X-RAY DIFFRACTION100
2.6265-2.70380.28171390.21552651X-RAY DIFFRACTION100
2.7038-2.7910.28951410.21062663X-RAY DIFFRACTION100
2.791-2.89070.30051400.20642671X-RAY DIFFRACTION100
2.8907-3.00640.26961380.19142623X-RAY DIFFRACTION100
3.0064-3.14310.23891430.182704X-RAY DIFFRACTION100
3.1431-3.30860.23121400.1752663X-RAY DIFFRACTION100
3.3086-3.51570.22611400.16092663X-RAY DIFFRACTION100
3.5157-3.78680.22371420.15722695X-RAY DIFFRACTION100
3.7868-4.16720.22131420.14832700X-RAY DIFFRACTION100
4.1672-4.76860.1851430.12622720X-RAY DIFFRACTION100
4.7686-6.0020.1861450.152752X-RAY DIFFRACTION100
6.002-32.83630.21791500.18382858X-RAY DIFFRACTION98

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