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- PDB-6b9y: Trastuzumab Fab v3 in complex with 5-phenyl meditope variant -

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Basic information

Entry
Database: PDB / ID: 6b9y
TitleTrastuzumab Fab v3 in complex with 5-phenyl meditope variant
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 / Immunoglobulin subtype / Immunoglobulin / Immunoglobulins and major histocompatibility complex proteins signature. / 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 / IGH@ protein
Similarity search - Component
Biological speciesHomo 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 11, 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

Downloads & links

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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)62,0295
Polymers62,0295
Non-polymers00
Water9,638535
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8090 Å2
ΔGint-45 kcal/mol
Surface area24080 Å2
Unit cell
Length a, b, c (Å)52.990, 104.600, 116.290
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


Mass: 23518.004 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (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
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: IGH@ / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: Q6GMX6
#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
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: 1758.977 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: 2.6 Å3/Da / Density % sol: 52.69 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1 M Tris pH 7.5, 15% PEG3350, 24 mM NaCl

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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: Jan 4, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.14→31.35 Å / Num. obs: 36407 / % possible obs: 99.9 % / Redundancy: 4.8 % / CC1/2: 0.994 / Rrim(I) all: 0.18 / Net I/σ(I): 9.1
Reflection shellResolution: 2.14→2.2 Å / Redundancy: 4.7 % / Mean I/σ(I) obs: 1.65 / Num. unique obs: 2655 / CC1/2: 0.568 / Rrim(I) all: 1.09 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ioi

4ioi


Resolution: 2.14→29.903 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.83
RfactorNum. reflection% reflection
Rfree0.2178 1821 5 %
Rwork0.1709 --
obs0.1733 36395 99.86 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 2.14→29.903 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4332 0 0 535 4867
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064516
X-RAY DIFFRACTIONf_angle_d0.8656153
X-RAY DIFFRACTIONf_dihedral_angle_d12.1932742
X-RAY DIFFRACTIONf_chiral_restr0.05685
X-RAY DIFFRACTIONf_plane_restr0.005801
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1399-2.19770.28351380.23972614X-RAY DIFFRACTION100
2.1977-2.26240.30691380.22552626X-RAY DIFFRACTION100
2.2624-2.33540.23721380.22112616X-RAY DIFFRACTION100
2.3354-2.41880.2611380.21352626X-RAY DIFFRACTION100
2.4188-2.51560.28251380.19742626X-RAY DIFFRACTION100
2.5156-2.630.22211390.19672641X-RAY DIFFRACTION100
2.63-2.76860.21731390.18832627X-RAY DIFFRACTION100
2.7686-2.94190.26361400.18912660X-RAY DIFFRACTION100
2.9419-3.16880.20131390.17082642X-RAY DIFFRACTION100
3.1688-3.48730.2331400.15922662X-RAY DIFFRACTION100
3.4873-3.99090.20451420.1422691X-RAY DIFFRACTION100
3.9909-5.02420.14491420.12332699X-RAY DIFFRACTION100
5.0242-29.90540.20841500.16692844X-RAY DIFFRACTION100
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.30180.5116-0.78462.72853.47856.6840.01720.15890.0167-0.12840.1782-0.1152-0.2995-0.0859-0.12360.15420.00040.00290.17460.03120.214618.990134.2549.9984
22.6072-0.0243-0.28222.54071.00911.2331-0.01780.07250.13290.0552-00.2626-0.1188-0.12160.02220.19010.0252-0.01950.19020.0210.192110.087728.14558.4763
30.9349-0.4489-0.55621.87881.7813.2065-0.02040.02680.10420.1089-0.00520.15710.0439-0.1537-0.01530.19110.00590.00460.20450.01620.18615.00726.459610.4865
40.61460.47161.87560.36171.43795.70940.0037-0.0747-0.17750.00150.07830.0399-0.0059-0.0141-0.15690.19610.0443-0.0130.1630.01430.178919.593337.774327.5483
52.9755-1.19791.0442.3048-0.1681.43780.2363-0.0068-0.00730.0303-0.0589-0.07050.31790.2437-0.14270.28710.0484-0.00190.187-0.03620.155331.162126.189341.8322
64.785-0.09533.38931.545-0.68973.73080.14080.23320.2326-0.1431-0.0732-0.26040.03570.6853-0.0190.25910.00270.05040.363-0.07130.294739.821127.279238.6584
75.7046-2.96861.17845.6167-0.52345.17040.2171-0.0433-0.6522-0.0723-0.20120.66620.5993-0.50420.03060.2854-0.03630.01020.21490.01040.283117.456931.157230.9129
84.5686-2.40811.81084.0165-1.31814.27150.06090.088-0.33770.23260.0448-0.22850.14180.4501-0.0420.33530.0763-0.08470.2834-0.0320.291839.720820.125844.8316
93.4982-3.64852.92456.716-2.93423.224-0.0562-0.15880.0570.33640.2053-0.3329-0.01050.0692-0.09420.2008-0.0034-0.03410.2197-0.04550.195634.803532.650947.2814
102.1587-0.8820.23472.129-0.02391.66970.05880.06750.0418-0.02530.01510.08190.0403-0.1327-0.07330.17380.01310.00340.18230.01640.196715.60357.45069.4774
110.6624-0.6084-0.37970.81060.95721.60390.0138-0.0008-0.1050.1164-0.04130.07340.1729-0.01490.04030.28630.0090.00770.1749-0.01660.209723.093415.875638.7361
124.6645-1.9444-3.50174.05671.59833.9217-0.1978-0.6246-0.39930.82270.0357-0.42780.60920.54690.18290.44950.03080.01390.27060.06080.271121.891211.31548.466
133.5121-4.722-1.26516.59190.85513.47370.1282-0.26930.05050.03990.013-0.004-0.24060.2261-0.10940.2664-0.0427-0.02220.2339-0.00960.383724.897544.388115.244
144.2585-1.3732-1.69582.5066-0.24212.40870.24120.29460.5243-0.079-0.1144-0.1726-0.34210.0811-0.08740.2643-0.0440.00580.23470.06790.301725.06843.92718.4345
156.3599-1.89960.58166.0170.31445.673-0.0511-0.36420.0420.14470.4979-0.043-0.5090.4058-0.46340.3449-0.0780.03050.37420.04740.351927.246949.204912.668
167.55190.12843.11832.3716-0.58424.10950.2620.4599-0.2076-0.5283-0.10680.25550.0553-0.2894-0.13050.33230.0166-0.04410.308-0.07340.285724.4218-13.6231-2.1765
172.8171-1.81631.35512.1454-0.82752.09230.18890.1868-0.1233-0.2699-0.12570.13370.27530.0294-0.07380.2385-0.0090.01320.1835-0.02620.232427.7907-8.58577.5603
186.8904-0.81884.25594.1301-0.57075.31520.02140.41050.1554-0.4554-0.1214-0.4122-0.2159-0.16850.10590.30160.0430.08970.2590.01740.195432.066-3.71421.4682
196.5097-5.5196-1.70195.58862.70052.1862-0.075-0.24760.62520.28980.3177-0.9073-0.47350.5468-0.2310.4565-0.0147-0.04170.3393-0.06560.389125.970322.876320.5424
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'A' and (resid 1 through 25 )
2X-RAY DIFFRACTION2chain 'A' and (resid 26 through 75 )
3X-RAY DIFFRACTION3chain 'A' and (resid 76 through 101 )
4X-RAY DIFFRACTION4chain 'A' and (resid 102 through 113 )
5X-RAY DIFFRACTION5chain 'A' and (resid 114 through 150 )
6X-RAY DIFFRACTION6chain 'A' and (resid 151 through 163 )
7X-RAY DIFFRACTION7chain 'A' and (resid 164 through 174 )
8X-RAY DIFFRACTION8chain 'A' and (resid 175 through 188 )
9X-RAY DIFFRACTION9chain 'A' and (resid 189 through 214 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 113 )
11X-RAY DIFFRACTION11chain 'B' and (resid 114 through 210 )
12X-RAY DIFFRACTION12chain 'B' and (resid 211 through 223 )
13X-RAY DIFFRACTION13chain 'E' and (resid 19 through 33 )
14X-RAY DIFFRACTION14chain 'E' and (resid 34 through 69 )
15X-RAY DIFFRACTION15chain 'E' and (resid 70 through 81 )
16X-RAY DIFFRACTION16chain 'C' and (resid 1 through 16 )
17X-RAY DIFFRACTION17chain 'C' and (resid 17 through 35 )
18X-RAY DIFFRACTION18chain 'C' and (resid 36 through 54 )
19X-RAY DIFFRACTION19chain 'D' and (resid 1 through 12 )

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