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- PDB-6u85: Site-specific lysine arylation as an alternative bioconjugation s... -

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Basic information

Entry
Database: PDB / ID: 6u85
TitleSite-specific lysine arylation as an alternative bioconjugation strategy for chemically programmed antibodies and antibody-drug conjugates
Components
  • Antibody Fab heavy chain
  • antibody Fab Light chain
KeywordsIMMUNE SYSTEM / Single chain Fv / ScFv / Antibody / ROR2 / Kringle domain / receptor tyrosine kinase-like orphan receptor / Phage display
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.78 Å
AuthorsPark, H. / Rader, C.
CitationJournal: Bioconjug.Chem. / Year: 2019
Title: Site-Specific Lysine Arylation as an Alternative Bioconjugation Strategy for Chemically Programmed Antibodies and Antibody-Drug Conjugates.
Authors: Hwang, D. / Tsuji, K. / Park, H. / Burke Jr., T.R. / Rader, C.
History
DepositionSep 4, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 13, 2019Provider: repository / Type: Initial release
Revision 1.1Dec 4, 2019Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Oct 11, 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 / software
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _software.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: Antibody Fab heavy chain
L: antibody Fab Light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0783
Polymers47,9862
Non-polymers921
Water43224
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3490 Å2
ΔGint-23 kcal/mol
Surface area20030 Å2
MethodPISA
Unit cell
Length a, b, c (Å)92.762, 92.762, 107.812
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number170
Space group name H-MP65
Space group name HallP65
Symmetry operation#1: x,y,z
#2: x-y,x,z+5/6
#3: y,-x+y,z+1/6
#4: -y,x-y,z+2/3
#5: -x+y,-x,z+1/3
#6: -x,-y,z+1/2

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Components

#1: Antibody Antibody Fab heavy chain


Mass: 24005.816 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#2: Antibody antibody Fab Light chain


Mass: 23979.693 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): HEK293 / Production host: Homo sapiens (human)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 24 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestN

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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: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 0.2 M Ammonium citrate dibasic, 20% w/v Polyethylene glycol 3,350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.9774 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Oct 2, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9774 Å / Relative weight: 1
ReflectionResolution: 2.78→44.76 Å / Num. obs: 12768 / % possible obs: 85.11 % / Redundancy: 5.8 % / Biso Wilson estimate: 55.76 Å2 / CC1/2: 0.994 / Rmerge(I) obs: 0.1934 / Net I/σ(I): 8.99
Reflection shellResolution: 2.78→2.88 Å / Rmerge(I) obs: 2.263 / Num. unique obs: 256 / CC1/2: 0.252

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Processing

Software
NameVersionClassification
PHENIX1.15.2_3472refinement
PHENIX1.15.2_3472refinement
XDSdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6DZR

6dzr


Resolution: 2.78→44.76 Å / SU ML: 0.4205 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 29.3718
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2592 521 4.6 %
Rwork0.2111 10800 -
obs0.2134 11321 85.13 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 65.25 Å2
Refinement stepCycle: LAST / Resolution: 2.78→44.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3331 0 6 24 3361
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00253417
X-RAY DIFFRACTIONf_angle_d0.53064643
X-RAY DIFFRACTIONf_chiral_restr0.0416517
X-RAY DIFFRACTIONf_plane_restr0.0059592
X-RAY DIFFRACTIONf_dihedral_angle_d14.99292032
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.78-3.060.4054910.33181778X-RAY DIFFRACTION56.47
3.06-3.50.37591500.27052921X-RAY DIFFRACTION92.84
3.5-4.410.23941400.19762891X-RAY DIFFRACTION91.21
4.41-44.760.19611400.17673210X-RAY DIFFRACTION99.85
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)
11.39554010706-1.904476687441.51016822693.92474132086-0.4954837202893.39705855169-0.395755161513-0.16792588622-0.1339005322880.1354052511530.248109848550.167208865699-0.350630841535-0.1878977491840.04550077052670.3016963798630.11258948520.1297274583820.2595042727240.007258395867840.279039213874-32.8224021508-13.161629899-3.98908336587
23.40444263678-1.68666789583-0.6012380148552.944294366750.546419418012.616367303860.1131222384020.09453792565350.04824424333630.0567527275970.06638448897390.25165057048-0.355195924058-0.251833280478-0.05797277131630.2461169461240.1925554838980.1338847050160.286977158648-0.005193045404770.177847234041-32.6639452855-14.8850043379-3.07216504573
31.287125790490.54374387962-0.375266914586.05563415453-3.210360688032.9285023525-0.273260549071-0.298338585726-0.3339119355670.1810599582360.178546053529-0.296135947980.329015659257-0.1887744783650.05439820908980.3128339760420.07237758587810.0474906844250.3502231459810.1175593247180.383687451508-27.9666124774-37.7563548272.23502699015
44.34084429136-0.0815404654182-2.870415679364.39650020004-3.349849823026.24063572695-0.03892241648160.126031214073-0.268808471978-0.2365983382060.06661030815670.2460342035030.674092029689-0.305989042954-0.08678155870850.381698887093-0.0633082942410.01544877849030.271137672647-0.01951192438890.20445998761-30.1480356282-46.61534393646.79289537176
58.136481409561.17311889682-2.781028393973.14880020943-2.449156734074.97826881077-0.07276640526-0.104644727190.4412024014270.343061127065-0.521474639576-1.21480707168-0.5675669105360.2413422261180.475676857850.4490735258930.02963623045-0.08125424450460.429665052479-0.04852454096230.567110561052-17.2781527636-14.827161971319.3605970679
64.0594678584-1.850616676530.8290250246784.642202362760.1701734613275.91674181015-0.05093209610090.2459172186670.223591039468-0.255556092041-0.210089118013-0.3507867456590.2189602032310.1184340337090.2211639513590.3306370143710.03531151719120.007745852457890.187157444767-9.25440312412E-50.174305437501-25.8530910604-11.10380762317.5315060184
70.640501981245-0.3891636770980.3507254760282.17576351352-1.065336090271.804692704750.128053113975-0.119748469107-0.108605686396-0.585891782801-0.361809355553-0.7224958165720.5983871258080.606250192010.04949783386580.2989225539510.1791965525620.09120625568020.5400489146690.1841387028550.443854219048-15.8784254203-44.055156199112.9701881141
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'H' and (resid 1 through 75 )
2X-RAY DIFFRACTION2chain 'H' and (resid 76 through 105 )
3X-RAY DIFFRACTION3chain 'H' and (resid 106 through 140 )
4X-RAY DIFFRACTION4chain 'H' and (resid 141 through 230 )
5X-RAY DIFFRACTION5chain 'L' and (resid 1 through 24 )
6X-RAY DIFFRACTION6chain 'L' and (resid 25 through 94 )
7X-RAY DIFFRACTION7chain 'L' and (resid 95 through 218 )

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