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- PDB-5t1k: Cetuximab Fab in complex with CQFDA(Ph)2STRRLKC -

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Basic information

Entry
Database: PDB / ID: 5t1k
TitleCetuximab Fab in complex with CQFDA(Ph)2STRRLKC
Components
  • (CETUXIMAB FAB HEAVY ...) x 2
  • CETUXIMAB FAB LIGHT CHAIN
  • CQFDA(PH)2STRRLKC PEPTIDE
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: 2.48 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
DepositionAug 19, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 26, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Sep 27, 2017Group: Data collection / Derived calculations / Category: diffrn_detector / pdbx_struct_oper_list
Item: _diffrn_detector.detector / _pdbx_struct_oper_list.symmetry_operation
Revision 1.3Dec 6, 2017Group: Database references / Category: citation
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
Revision 2.0Dec 25, 2019Group: Derived calculations / Polymer sequence / Category: entity_poly / pdbx_struct_mod_residue
Item: _entity_poly.pdbx_seq_one_letter_code_can / _pdbx_struct_mod_residue.parent_comp_id
Revision 2.1Oct 4, 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
Revision 2.2Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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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: CQFDA(PH)2STRRLKC PEPTIDE
F: CQFDA(PH)2STRRLKC PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,77212
Polymers97,1756
Non-polymers5976
Water9,332518
1
A: CETUXIMAB FAB LIGHT CHAIN
B: CETUXIMAB FAB HEAVY CHAIN
E: CQFDA(PH)2STRRLKC PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8646
Polymers48,5793
Non-polymers2853
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-47 kcal/mol
Surface area19040 Å2
MethodPISA
2
C: CETUXIMAB FAB LIGHT CHAIN
D: CETUXIMAB FAB HEAVY CHAIN
F: CQFDA(PH)2STRRLKC PEPTIDE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,9086
Polymers48,5963
Non-polymers3123
Water543
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5750 Å2
ΔGint-40 kcal/mol
Surface area18720 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.280, 83.250, 212.300
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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Protein/peptide , 1 types, 2 molecules EF

#4: Protein/peptide CQFDA(PH)2STRRLKC PEPTIDE


Mass: 1582.868 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)

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Antibody , 3 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: Mus musculus (house mouse)
#2: Antibody CETUXIMAB FAB HEAVY CHAIN


Mass: 23708.475 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Mus musculus (house mouse)
#3: Antibody CETUXIMAB FAB HEAVY CHAIN


Mass: 23725.504 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus, Homo sapiens / Production host: Mus musculus (house mouse)

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Non-polymers , 3 types, 524 molecules

#5: Chemical
ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 5 / 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.: 518 / 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: 2.92 Å3/Da / Density % sol: 57.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 0.1 CITRIC ACID, 0.1 M SODIUM HYDROGEN PHOSPHATE, 0.5 M POTASSIUM HYDROGEN PHOSPHATE, 1.6 M SODIUM DIHYDROGEN PHOSPHATE, PH 5.5
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: Sep 2, 2011
RadiationMonochromator: VARIMAX / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.48→33.2 Å / Num. obs: 41117 / % possible obs: 99.1 % / Observed criterion σ(I): 2 / Redundancy: 4.6 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 23.5
Reflection shellResolution: 2.48→2.54 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.248 / Mean I/σ(I) obs: 4.7 / % possible all: 90.3

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
PHENIX1.8.1_1168refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4gw1

4gw1


Resolution: 2.48→33.2 Å / SU ML: 0.25 / Cross valid method: FREE R-VALUE / σ(F): 2 / Phase error: 20.11
RfactorNum. reflection% reflection
Rfree0.213 2055 5 %
Rwork0.16 --
obs0.163 41103 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.2 Å
Refinement stepCycle: LAST / Resolution: 2.48→33.2 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6772 0 33 518 7323
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0087038
X-RAY DIFFRACTIONf_angle_d1.1499581
X-RAY DIFFRACTIONf_dihedral_angle_d13.7952538
X-RAY DIFFRACTIONf_chiral_restr0.0731074
X-RAY DIFFRACTIONf_plane_restr0.0051228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.48-2.5340.26291210.20292306X-RAY DIFFRACTION89
2.534-2.59730.27951350.18642560X-RAY DIFFRACTION100
2.5973-2.66750.28581370.17882597X-RAY DIFFRACTION100
2.6675-2.7460.24251340.18272561X-RAY DIFFRACTION100
2.746-2.83450.26051370.18312605X-RAY DIFFRACTION100
2.8345-2.93580.28081370.1792599X-RAY DIFFRACTION100
2.9358-3.05330.25731370.17482596X-RAY DIFFRACTION100
3.0533-3.19210.22261370.17082615X-RAY DIFFRACTION100
3.1921-3.36030.22931370.16672596X-RAY DIFFRACTION100
3.3603-3.57060.2051370.1552606X-RAY DIFFRACTION100
3.5706-3.84590.19361370.15242607X-RAY DIFFRACTION100
3.8459-4.23220.19041400.13822650X-RAY DIFFRACTION100
4.2322-4.8430.15691400.11892662X-RAY DIFFRACTION100
4.843-6.09550.16981410.13962679X-RAY DIFFRACTION100
6.0955-33.19060.20421480.18962809X-RAY DIFFRACTION99

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