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- PDB-6bae: Trastuzumab Fab v3 in complex with CQFDLSTRRLKC -

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Basic information

Entry
Database: PDB / ID: 6bae
TitleTrastuzumab Fab v3 in complex with CQFDLSTRRLKC
Components
  • (Trastuzumab Fab ...) x 2
  • Immunoglobulin G binding protein A
  • Protein L
  • meditope
KeywordsIMMUNE SYSTEM / monoclonal antibody / Fab / meditope
Function / homology
Function and homology information


IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / IgG binding / Classical antibody-mediated complement activation / Initial triggering of complement ...IgD immunoglobulin complex / IgM immunoglobulin complex / IgA immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / IgG binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin binding / FCGR activation / immunoglobulin mediated immune response / Role of phospholipids in phagocytosis / Role of LAT2/NTAL/LAB on calcium mobilization / Scavenging of heme from plasma / immunoglobulin complex, circulating / immunoglobulin receptor binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / complement activation, classical pathway / Regulation of Complement cascade / Cell surface interactions at the vascular wall / FCERI mediated MAPK activation / FCGR3A-mediated phagocytosis / antigen binding / B cell receptor signaling pathway / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / antibacterial humoral response / adaptive immune response / Potential therapeutics for SARS / blood microparticle / immune response / extracellular space / extracellular exosome / extracellular region / plasma membrane
Similarity search - Function
Protein G-related albumin-binding (GA) module / Extracellular matrix-binding protein ebh, GA module / GA module / GA module / Protein L, Ig light chain-binding / Protein L b1 domain / Repeat of unknown function DUF5633 / Family of unknown function (DUF5633) / Octapeptide repeat / Octapeptide repeat ...Protein G-related albumin-binding (GA) module / Extracellular matrix-binding protein ebh, GA module / GA module / GA module / Protein L, Ig light chain-binding / Protein L b1 domain / Repeat of unknown function DUF5633 / Family of unknown function (DUF5633) / Octapeptide repeat / Octapeptide repeat / Immunoglobulin FC, subunit C / Protein A, Ig-binding domain / B domain / Ubiquitin-like (UB roll) - #10 / GA-like domain / GA-like domain / Lysin motif / LysM domain superfamily / LysM domain / LysM domain profile. / LysM domain / Immunoglobulin/albumin-binding domain superfamily / YSIRK type signal peptide / YSIRK Gram-positive signal peptide / LPXTG cell wall anchor motif / Gram-positive cocci surface proteins LPxTG motif profile. / LPXTG cell wall anchor domain / Single alpha-helices involved in coiled-coils or other helix-helix interfaces / Immunoglobulin V-Type / Immunoglobulin V-set domain / Immunoglobulin V-set domain / Ubiquitin-like (UB roll) / Immunoglobulin/major histocompatibility complex, conserved site / Immunoglobulins and major histocompatibility complex proteins signature. / Immunoglobulin subtype / Immunoglobulin / Immunoglobulin C-Type / Immunoglobulin C1-set / Immunoglobulin C1-set domain / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Immunoglobulins / Roll / Immunoglobulin-like fold / Up-down Bundle / Immunoglobulin-like / Sandwich / Mainly Beta / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Immunoglobulin kappa constant / Immunoglobulin G-binding protein A / Immunoglobulin G binding protein A / Protein L / IgG H chain
Similarity search - Component
Biological speciesMus musculus (house mouse)
Homo sapiens (human)
Finegoldia magna (bacteria)
Staphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.14 Å
AuthorsBzymek, K.P. / King, J.D. / Williams, J.C.
CitationJournal: Bioconjug. Chem. / Year: 2018
Title: Template-Catalyzed, Disulfide Conjugation of Monoclonal Antibodies Using a Natural Amino Acid Tag.
Authors: King, J.D. / Ma, Y. / Kuo, Y.C. / Bzymek, K.P. / Goodstein, L.H. / Meyer, K. / Moore, R.E. / Crow, D. / Colcher, D.M. / Singh, G. / Horne, D.A. / Williams, J.C.
History
DepositionOct 12, 2017Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 5, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Trastuzumab Fab light chain
B: Trastuzumab Fab heavy chain
E: Protein L
C: Immunoglobulin G binding protein A
D: meditope


Theoretical massNumber of molelcules
Total (without water)61,7675
Polymers61,7675
Non-polymers00
Water9,638535
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8380 Å2
ΔGint-40 kcal/mol
Surface area24060 Å2
Unit cell
Length a, b, c (Å)53.310, 104.940, 117.630
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 , 3 types, 3 molecules ABC

#1: Antibody Trastuzumab Fab light chain / Ig kappa chain C region / Ig kappa chain C region AG / Ig kappa chain C region CUM / Ig kappa chain ...Ig kappa chain C region / Ig kappa chain C region AG / Ig kappa chain C region CUM / Ig kappa chain C region EU / Ig kappa chain C region OU / Ig kappa chain C region ROY / Ig kappa chain C region TI


Mass: 23518.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Gene: IGKC / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P01834
#2: Antibody Trastuzumab Fab heavy chain


Mass: 23806.670 Da / Num. of mol.: 1 / Mutation: A175C, R217K
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse), (gene. exp.) Homo sapiens (human)
Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: S6B291
#4: Antibody Immunoglobulin G binding protein A


Mass: 6037.530 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Staphylococcus aureus (bacteria) / Gene: spa / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q2UW42, UniProt: P02976*PLUS

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Protein / Protein/peptide / Non-polymers , 3 types, 537 molecules ED

#3: Protein Protein L


Mass: 6907.657 Da / Num. of mol.: 1 / Mutation: T17I, D38A, Y56N, T57H, I58M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Finegoldia magna (bacteria) / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: Q51918
#5: Protein/peptide meditope


Mass: 1496.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others)
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 535 / 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: 2.66 Å3/Da / Density % sol: 53.82 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH 7.5, 24 mM NaCl, 15% PEG 3350

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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: Dec 7, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.14→33.53 Å / Num. obs: 37070 / % possible obs: 99.7 % / Redundancy: 5.1 % / CC1/2: 0.995 / Rrim(I) all: 0.152 / Net I/σ(I): 10.3
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 5.1 % / Num. unique obs: 2675 / CC1/2: 0.611 / Rrim(I) all: 0.931 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX1.11.1_2575refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ioi

4ioi


Resolution: 2.14→33.529 Å / SU ML: 0.22 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 21.18
RfactorNum. reflection% reflection
Rfree0.2241 1853 5 %
Rwork0.173 --
obs0.1756 37064 99.74 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.14→33.529 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4325 0 0 535 4860
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0074486
X-RAY DIFFRACTIONf_angle_d0.8726110
X-RAY DIFFRACTIONf_dihedral_angle_d12.5582716
X-RAY DIFFRACTIONf_chiral_restr0.051681
X-RAY DIFFRACTIONf_plane_restr0.005795
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1399-2.19780.26991380.22052620X-RAY DIFFRACTION100
2.1978-2.26240.26931420.21252689X-RAY DIFFRACTION100
2.2624-2.33540.30311400.21182668X-RAY DIFFRACTION100
2.3354-2.41890.27921420.20632700X-RAY DIFFRACTION100
2.4189-2.51570.26971410.20892671X-RAY DIFFRACTION100
2.5157-2.63020.24751410.19762693X-RAY DIFFRACTION100
2.6302-2.76880.2811420.19642695X-RAY DIFFRACTION100
2.7688-2.94210.28291430.19062703X-RAY DIFFRACTION100
2.9421-3.16910.25281420.18922706X-RAY DIFFRACTION100
3.1691-3.48780.17681430.16322721X-RAY DIFFRACTION100
3.4878-3.99180.20241440.14292724X-RAY DIFFRACTION100
3.9918-5.02650.16661450.12962761X-RAY DIFFRACTION99
5.0265-33.5330.19471500.16582860X-RAY DIFFRACTION98

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