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- PDB-5esq: Cetuximab Fab in complex with cyclic beta-alanine-linked meditope -

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Basic information

Entry
Database: PDB / ID: 5esq
TitleCetuximab Fab in complex with cyclic beta-alanine-linked meditope
Components
  • Cetuximab Fab heavy chain
  • Cetuximab Fab light chain
  • Cyclic beta-alanine-linked meditope
KeywordsIMMUNE SYSTEM / antibody / anti-EGFR
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / PHOSPHATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
synthetic construct (others)
MethodX-RAY DIFFRACTION / Resolution: 2.55 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
DepositionNov 16, 2015Deposition 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 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id

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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: Cyclic beta-alanine-linked meditope
F: Cyclic beta-alanine-linked meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,41312
Polymers96,8446
Non-polymers5706
Water6,323351
1
A: Cetuximab Fab light chain
B: Cetuximab Fab heavy chain
E: Cyclic beta-alanine-linked meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7076
Polymers48,4223
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5500 Å2
ΔGint-43 kcal/mol
Surface area18650 Å2
MethodPISA
2
C: Cetuximab Fab light chain
D: Cetuximab Fab heavy chain
F: Cyclic beta-alanine-linked meditope
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7076
Polymers48,4223
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5540 Å2
ΔGint-46 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.140, 82.570, 212.070
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 (house mouse) / 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 (house mouse) / Production host: unidentified (others)
#3: Protein/peptide Cyclic beta-alanine-linked meditope


Mass: 1408.626 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.: 6 / Source method: obtained synthetically / Formula: PO4
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 351 / Source method: isolated from a natural source / Formula: H2O
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: 2.9 Å3/Da / Density % sol: 57.58 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
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: Sep 8, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.55→34.26 Å / Num. obs: 37518 / % possible obs: 99.2 % / Redundancy: 5.49 % / Rmerge(I) obs: 0.076 / Net I/σ(I): 20.57
Reflection shellResolution: 2.55→2.62 Å / Mean I/σ(I) obs: 4.9 / % possible all: 93

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementResolution: 2.55→34.26 Å / SU ML: 0.3 / Cross valid method: FREE R-VALUE / σ(F): 1.99 / Phase error: 22.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2419 1868 4.98 %
Rwork0.1898 --
obs0.1923 37508 99.24 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.55→34.26 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6683 0 30 351 7064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0046939
X-RAY DIFFRACTIONf_angle_d0.7579457
X-RAY DIFFRACTIONf_dihedral_angle_d11.1112470
X-RAY DIFFRACTIONf_chiral_restr0.0491067
X-RAY DIFFRACTIONf_plane_restr0.0041211
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.5458-2.61460.31971430.24442534X-RAY DIFFRACTION93
2.6146-2.69150.31121420.22892705X-RAY DIFFRACTION100
2.6915-2.77830.29621430.22212716X-RAY DIFFRACTION100
2.7783-2.87760.28321500.21552710X-RAY DIFFRACTION100
2.8776-2.99270.251340.21252741X-RAY DIFFRACTION100
2.9927-3.12880.29231610.21382695X-RAY DIFFRACTION100
3.1288-3.29370.27561380.20372753X-RAY DIFFRACTION100
3.2937-3.49980.26441410.19682735X-RAY DIFFRACTION100
3.4998-3.76970.26121410.19272768X-RAY DIFFRACTION99
3.7697-4.14850.21721320.17382758X-RAY DIFFRACTION100
4.1485-4.74750.18781340.14362802X-RAY DIFFRACTION100
4.7475-5.97610.1931330.16032817X-RAY DIFFRACTION100
5.9761-34.26230.19971760.19352906X-RAY DIFFRACTION99

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