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- PDB-6bah: Trastuzumab Fab v3 with 5-diphenyl meditope variant -

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Basic information

Entry
Database: PDB / ID: 6bah
TitleTrastuzumab Fab v3 with 5-diphenyl meditope variant
Components
  • (Trastuzumab Fab ...) x 2
  • Immunoglobulin G binding protein A
  • Protein L
  • meditope
KeywordsIMMUNE SYSTEM / monoclonal antibody / Fab
Function / homology
Function and homology information


IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / cell envelope / IgG binding / Classical antibody-mediated complement activation ...IgD immunoglobulin complex / IgA immunoglobulin complex / IgM immunoglobulin complex / IgE immunoglobulin complex / CD22 mediated BCR regulation / IgG immunoglobulin complex / Fc epsilon receptor (FCERI) signaling / cell envelope / IgG binding / Classical antibody-mediated complement activation / Initial triggering of complement / immunoglobulin binding / immunoglobulin mediated immune response / FCGR activation / Role of LAT2/NTAL/LAB on calcium mobilization / Role of phospholipids in phagocytosis / Scavenging of heme from plasma / antigen binding / FCERI mediated Ca+2 mobilization / FCGR3A-mediated IL10 synthesis / Antigen activates B Cell Receptor (BCR) leading to generation of second messengers / Regulation of Complement cascade / Cell surface interactions at the vascular wall / B cell receptor signaling pathway / FCGR3A-mediated phagocytosis / FCERI mediated MAPK activation / Regulation of actin dynamics for phagocytic cup formation / FCERI mediated NF-kB activation / Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell / blood microparticle / adaptive immune response / Potential therapeutics for SARS / 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) / Immunoglobulin FC, subunit C / 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) / Immunoglobulin FC, subunit C / Octapeptide repeat / Octapeptide repeat / 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 subtype / Immunoglobulin / Immunoglobulin/major histocompatibility complex, conserved site / 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 / Roll / Immunoglobulin-like fold / Immunoglobulins / 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 speciesMus musculus (house mouse)
Homo sapiens (human)
Finegoldia magna (bacteria)
Staphylococcus aureus (bacteria)
synthetic construct (others)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 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
Revision 1.2Nov 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: Trastuzumab Fab light chain,Immunoglobulin kappa constant
B: Trastuzumab Fab heavy chain,IGH@ protein
E: Protein L
C: Immunoglobulin G binding protein A
D: meditope


Theoretical massNumber of molelcules
Total (without water)61,8625
Polymers61,8625
Non-polymers00
Water12,142674
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8300 Å2
ΔGint-38 kcal/mol
Surface area24130 Å2
Unit cell
Length a, b, c (Å)53.410, 105.150, 116.980
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,Immunoglobulin kappa constant / 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,IGH@ protein


Mass: 23806.670 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: 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, 676 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: 1591.790 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.: 674 / 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: 2.65 Å3/Da / Density % sol: 53.67 %
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: Jul 26, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→33.6 Å / Num. obs: 52561 / % possible obs: 99.7 % / Redundancy: 5.1 % / CC1/2: 0.998 / Rrim(I) all: 0.115 / Net I/σ(I): 13.2
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 1.7 / Num. unique obs: 3714 / CC1/2: 0.623 / Rrim(I) all: 1.06 / % possible all: 97.1

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Processing

Software
NameVersionClassification
PHENIX(1.12_2829: ???)refinement
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4ioi

4ioi


Resolution: 1.9→33.575 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 18.66 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1942 2627 5 %
Rwork0.1642 --
obs0.1657 52555 99.71 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.9→33.575 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4338 0 0 674 5012
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0064505
X-RAY DIFFRACTIONf_angle_d0.8546143
X-RAY DIFFRACTIONf_dihedral_angle_d13.0952739
X-RAY DIFFRACTIONf_chiral_restr0.054684
X-RAY DIFFRACTIONf_plane_restr0.005799
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.9001-1.93470.32291290.27112467X-RAY DIFFRACTION96
1.9347-1.97190.27591390.23312630X-RAY DIFFRACTION100
1.9719-2.01210.25081330.21922554X-RAY DIFFRACTION100
2.0121-2.05590.22091390.20092628X-RAY DIFFRACTION100
2.0559-2.10370.22011360.19312599X-RAY DIFFRACTION100
2.1037-2.15630.23341370.18452600X-RAY DIFFRACTION100
2.1563-2.21460.19051370.17352609X-RAY DIFFRACTION100
2.2146-2.27980.20841370.16972595X-RAY DIFFRACTION100
2.2798-2.35330.20791370.16772610X-RAY DIFFRACTION100
2.3533-2.43740.18541390.1722643X-RAY DIFFRACTION100
2.4374-2.5350.20361380.1662605X-RAY DIFFRACTION100
2.535-2.65030.21681370.16922611X-RAY DIFFRACTION100
2.6503-2.790.22341390.17022637X-RAY DIFFRACTION100
2.79-2.96470.19871390.16972644X-RAY DIFFRACTION100
2.9647-3.19340.20571390.16412646X-RAY DIFFRACTION100
3.1934-3.51440.19921400.1522652X-RAY DIFFRACTION100
3.5144-4.02230.1611410.13952673X-RAY DIFFRACTION100
4.0223-5.06480.13441410.12152697X-RAY DIFFRACTION100
5.0648-33.58050.17431500.16362828X-RAY DIFFRACTION99
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)
10.95730.7729-0.36552.72763.0865.5643-0.0045-0.01830.0326-0.04050.2287-0.1099-0.30490.22-0.21660.16030.0161-0.00510.13620.0330.177219.255634.466110.0224
22.0457-0.06070.45242.25850.77040.417-0.00720.07880.12110.0568-0.0210.2322-0.1182-0.17430.01130.08490.02240.00140.15560.02170.171610.356728.43438.2193
30.8178-0.6544-0.34922.31091.08612.1154-0.0461-0.01120.04650.20450.06580.12680.0406-0.09180.03290.1557-0.00650.01350.1580.03210.153815.256226.354210.2054
40.20390.2710.9170.35211.19544.0546-0.00840.0420.0178-0.1159-0.122-0.0285-0.09240.0350.10360.21340.03680.00680.16990.00320.151620.035837.944527.7243
52.849-0.84650.02334.2771-0.64212.34510.0273-0.1401-0.26820.93090.0573-0.15630.39080.1185-0.02770.35970.0698-0.10350.2171-0.03690.176931.933218.452948.5806
64.0495-2.97292.14832.7811-1.90892.24070.24270.2530.0864-0.1624-0.2244-0.15750.23780.3878-0.00890.19820.0449-0.0010.2083-0.04420.11231.681430.676838.5166
74.02890.40623.06721.36170.09194.18680.01460.1170.2249-0.12590.0177-0.32190.02160.7287-0.02770.17740.04970.01390.3379-0.05680.266240.277827.393438.9897
85.3367-3.43173.79343.938-2.27974.60870.29320.0915-0.2044-0.0381-0.0643-0.0070.36920.3079-0.20310.17640.0318-0.00890.1766-0.02130.128230.195725.381639.0263
92.6701-2.54882.17195.4461-2.7773.4383-0.0854-0.19670.11510.42340.2289-0.46480.07430.096-0.11360.21180.031-0.06960.1828-0.03990.162735.277732.746947.5987
102.3668-1.39540.32292.1163-0.21881.18210.07740.1490.0382-0.035-0.01480.10140.0084-0.0905-0.05950.1140.01320.00530.14410.01190.148815.94357.54619.3038
110.1213-0.06780.01960.46130.80241.46890.0268-0.0223-0.02110.19730.1017-0.05450.22360.1629-0.14220.21110.0372-0.03280.1533-0.00870.134426.43814.274236.4373
121.6742-1.5506-0.90762.60511.59322.64160.0146-0.0095-0.16560.2423-0.07140.12550.4185-0.01930.03990.2616-0.00040.0040.1521-0.0150.153722.003715.595840.9357
133.2471-4.4043-1.25296.56810.72913.83750.1267-0.4673-0.07350.15320.11030.1067-0.49440.3718-0.20090.2306-0.07130.03790.1839-0.01240.365325.326744.53515.3137
146.8538-1.3392-4.0931.35630.82415.9159-0.0612-0.4890.03460.170.0615-0.1131-0.02620.65650.00420.1692-0.0344-0.00570.19330.00230.219826.62239.597814.6164
157.144-2.271-0.61823.0452-0.04792.38750.13790.73950.5485-0.175-0.0756-0.0635-0.3537-0.0527-0.01350.2027-0.03830.0140.23730.09360.262524.635942.62825.5192
165.5607-3.35420.75414.1995-0.02265.97420.16330.07210.92220.43340.0537-0.2128-0.93780.718-0.07320.4306-0.14440.06080.29790.08430.49927.100450.556411.1676
179.37370.51553.97011.5612-0.38763.65130.19540.5127-0.0866-0.3915-0.18770.49160.2641-0.40340.01030.30660.0261-0.01920.3112-0.06290.261624.3736-13.7685-2.0353
182.5777-1.69570.47112.2769-0.31461.81450.14610.1042-0.1752-0.2421-0.14770.13250.0474-0.07510.00410.16890.01560.0040.1288-0.02360.153427.8515-8.54867.6143
196.4672-1.91884.65663.9-1.36524.41740.30730.36670.3539-0.6693-0.3282-0.4994-0.091-0.01250.06410.2640.09180.07290.22750.02690.156232.2459-3.64881.6456
202.7058-2.70941.68159.0618-0.50616.208-0.19960.15060.13791.34580.2366-0.7609-0.2010.86760.01010.41670.0379-0.11160.2736-0.04480.313325.256922.15321.3175
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 128 )
6X-RAY DIFFRACTION6chain 'A' and (resid 129 through 150 )
7X-RAY DIFFRACTION7chain 'A' and (resid 151 through 163 )
8X-RAY DIFFRACTION8chain 'A' and (resid 164 through 188 )
9X-RAY DIFFRACTION9chain 'A' and (resid 189 through 214 )
10X-RAY DIFFRACTION10chain 'B' and (resid 1 through 110 )
11X-RAY DIFFRACTION11chain 'B' and (resid 111 through 141 )
12X-RAY DIFFRACTION12chain 'B' and (resid 142 through 223 )
13X-RAY DIFFRACTION13chain 'E' and (resid 19 through 33 )
14X-RAY DIFFRACTION14chain 'E' and (resid 34 through 42 )
15X-RAY DIFFRACTION15chain 'E' and (resid 43 through 61 )
16X-RAY DIFFRACTION16chain 'E' and (resid 62 through 81 )
17X-RAY DIFFRACTION17chain 'C' and (resid 1 through 16 )
18X-RAY DIFFRACTION18chain 'C' and (resid 17 through 35 )
19X-RAY DIFFRACTION19chain 'C' and (resid 36 through 54 )
20X-RAY DIFFRACTION20chain 'D' and (resid 0 through 12 )

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