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- PDB-9axr: Crystal Structure of HY18-5B1_Ch Fab in Complex with Fentanyl -

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Basic information

Entry
Database: PDB / ID: 9axr
TitleCrystal Structure of HY18-5B1_Ch Fab in Complex with Fentanyl
Components
  • HY18-5B1_Ch Fab Heavy Chain
  • HY18-5B1_Ch 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: 3.3 Å
AuthorsMcGovern, M.R. / Rodarte, 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 30, 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
A: HY18-5B1_Ch Fab Heavy Chain
B: HY18-5B1_Ch Fab Light Chain
H: HY18-5B1_Ch Fab Heavy Chain
L: HY18-5B1_Ch Fab Light Chain
C: HY18-5B1_Ch Fab Heavy Chain
D: HY18-5B1_Ch Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)145,8997
Polymers145,5626
Non-polymers3361
Water00
1
A: HY18-5B1_Ch Fab Heavy Chain
B: HY18-5B1_Ch Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)48,5212
Polymers48,5212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3040 Å2
ΔGint-25 kcal/mol
Surface area21600 Å2
MethodPISA
2
H: HY18-5B1_Ch Fab Heavy Chain
L: HY18-5B1_Ch Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8573
Polymers48,5212
Non-polymers3361
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3670 Å2
ΔGint-27 kcal/mol
Surface area20260 Å2
MethodPISA
3
C: HY18-5B1_Ch Fab Heavy Chain
D: HY18-5B1_Ch Fab Light Chain


Theoretical massNumber of molelcules
Total (without water)48,5212
Polymers48,5212
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3210 Å2
ΔGint-21 kcal/mol
Surface area21010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)114.635, 114.635, 90.951
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Space group name HallP31

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Components

#1: Antibody HY18-5B1_Ch Fab Heavy Chain


Mass: 24925.697 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody HY18-5B1_Ch Fab Light Chain


Mass: 23595.084 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: 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
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: 2.37 Å3/Da / Density % sol: 48.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop
Details: 25% PEG 3350, 0.2M ammonium sulfate, 0.1M Bis-Tris pH 5.5

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Data collection

DiffractionMean temperature: 100 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 27, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97918 Å / Relative weight: 1
ReflectionResolution: 3.3→48.49 Å / Num. obs: 20115 / % possible obs: 99.9 % / Redundancy: 5.2 % / CC1/2: 0.946 / Rmerge(I) obs: 0.36 / Rpim(I) all: 0.173 / Rrim(I) all: 0.4 / Χ2: 2.04 / Net I/σ(I): 8.2 / Num. measured all: 105196
Reflection shellResolution: 3.3→3.56 Å / % possible obs: 100 % / Redundancy: 5 % / Rmerge(I) obs: 1.024 / Num. measured all: 20841 / Num. unique obs: 4177 / CC1/2: 0.55 / Rpim(I) all: 0.508 / Rrim(I) all: 1.145 / Χ2: 1.22 / Net I/σ(I) obs: 2.1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
HKL-2000data scaling
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.3→48.49 Å / Cross valid method: FREE R-VALUE / σ(F): 118.65 / Phase error: 49.8346
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.3164 900 4.48 %
Rwork0.2779 19198 -
obs0.2969 20098 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 94.44 Å2
Refinement stepCycle: LAST / Resolution: 3.3→48.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9131 0 25 0 9156
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00259346
X-RAY DIFFRACTIONf_angle_d0.568312823
X-RAY DIFFRACTIONf_chiral_restr0.04171534
X-RAY DIFFRACTIONf_plane_restr0.00461663
X-RAY DIFFRACTIONf_dihedral_angle_d13.00873096
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3.3-3.510.40951470.37083204X-RAY DIFFRACTION95.58
3.51-3.780.41591580.35663187X-RAY DIFFRACTION95.28
3.78-4.160.3631620.34123190X-RAY DIFFRACTION95.11
4.16-4.760.29781180.29663247X-RAY DIFFRACTION96.49
4.76-5.990.33891200.28233223X-RAY DIFFRACTION96.38
6-48.490.31011950.25463147X-RAY DIFFRACTION94.08

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