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- PDB-9axo: Crystal Structure of Antibody HY11-7E1_Ch2 Fab in Complex with Fe... -

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Basic information

Entry
Database: PDB / ID: 9axo
TitleCrystal Structure of Antibody HY11-7E1_Ch2 Fab in Complex with Fentanyl
Components
  • HY11-7E1_Ch2 Fab Heavy Chain
  • HY11-7E1_Ch2 Fab Light Chain
KeywordsIMMUNE SYSTEM / opioids / mAb / fentanyl / cross-reactive
Function / homologyChem-7V7
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.1 Å
AuthorsRodarte, J.V. / Pancera, M.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)UG3 DA047711 United States
CitationJournal: Acs Omega / Year: 2024
Title: Structure-Based Engineering of Monoclonal Antibodies for Improved Binding to Counteract the Effects of Fentanyl and Carfentanil.
Authors: Rodarte, J. / Baehr, C. / Hicks, D. / McGovern, M. / Zhang, Y. / Silva-Ortiz, P. / Hannon, B. / Duddu, S. / Pancera, M. / Pravetoni, M.
History
DepositionMar 6, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 2, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification
Revision 1.2Mar 12, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: HY11-7E1_Ch2 Fab Heavy Chain
L: HY11-7E1_Ch2 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)50,18817
Polymers48,5622
Non-polymers1,62615
Water2,360131
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6760 Å2
ΔGint-33 kcal/mol
Surface area19680 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.519, 60.519, 259.857
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212
Components on special symmetry positions
IDModelComponents
11H-473-

HOH

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Components

#1: Antibody HY11-7E1_Ch2 Fab Heavy Chain


Mass: 25129.043 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody HY11-7E1_Ch2 Fab Light Chain


Mass: 23432.854 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 14 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical ChemComp-7V7 / N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide


Mass: 336.471 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H28N2O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 131 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.45 Å3/Da / Density % sol: 49.79 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 1.4M ammonium sulfate, 0.1M Bis-Tris pH 5.5, 0.01M NiCl2

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97918 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Jul 30, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 2.1→49.61 Å / Num. obs: 29502 / % possible obs: 100 % / Redundancy: 1.8 % / CC1/2: 0.996 / Rmerge(I) obs: 0.04 / Rpim(I) all: 0.04 / Rrim(I) all: 0.056 / Χ2: 1.35 / Net I/σ(I): 20.6 / Num. measured all: 54213
Reflection shellResolution: 2.1→2.16 Å / % possible obs: 100 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.262 / Num. measured all: 4460 / Num. unique obs: 2367 / CC1/2: 0.828 / Rpim(I) all: 0.262 / Rrim(I) all: 0.371 / Χ2: 0.58 / Net I/σ(I) obs: 2.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→49.61 Å / SU ML: 0.26 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 27.08 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2781 1469 5 %
Rwork0.2315 --
obs0.2339 29357 99.83 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.1→49.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3301 0 109 131 3541
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0053480
X-RAY DIFFRACTIONf_angle_d0.8584704
X-RAY DIFFRACTIONf_dihedral_angle_d13.1951238
X-RAY DIFFRACTIONf_chiral_restr0.053517
X-RAY DIFFRACTIONf_plane_restr0.007590
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.1-2.180.34861440.32532721X-RAY DIFFRACTION100
2.18-2.260.29961420.28542709X-RAY DIFFRACTION100
2.26-2.370.31891430.28552717X-RAY DIFFRACTION100
2.37-2.490.30361440.27672737X-RAY DIFFRACTION100
2.49-2.650.32251450.26382763X-RAY DIFFRACTION100
2.65-2.850.27881460.25182765X-RAY DIFFRACTION100
2.85-3.140.31671470.25362769X-RAY DIFFRACTION100
3.14-3.590.291480.22232816X-RAY DIFFRACTION100
3.59-4.520.24351500.19532855X-RAY DIFFRACTION100
4.52-49.610.25311600.2123036X-RAY DIFFRACTION99

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