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- PDB-8tfq: Fab from C10-S66K antibody in complex with fentanyl -

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Basic information

Entry
Database: PDB / ID: 8tfq
TitleFab from C10-S66K antibody in complex with fentanyl
Components
  • Heavy chain from Fab of C10_S66K antibody
  • Light chain from Fab of C10_S66K antibody
KeywordsIMMUNE SYSTEM / Antibody / fentanyl / opioid.
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-7V7
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsPholcharee, T. / Wilson, I.A.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)U01DA046232 United States
Citation
Journal: Acs Chem Neurosci / Year: 2023
Title: An Engineered Human-Antibody Fragment with Fentanyl Pan-Specificity That Reverses Carfentanil-Induced Respiratory Depression.
Authors: Eubanks, L.M. / Pholcharee, T. / Oyen, D. / Natori, Y. / Zhou, B. / Wilson, I.A. / Janda, K.D.
#1: Journal: Biorxiv / Year: 2023
Title: An Engineered Human-Antibody Fragment with Fentanyl Pan-Specificity that Reverses Carfentanil-Induced Respiratory Depression.
Authors: Eubanks, L.M. / Pholcharee, T. / Oyen, D. / Natori, Y. / Zhou, B. / Wilson, I.A. / Janda, K.D.
History
DepositionJul 11, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 16, 2023Provider: repository / Type: Initial release
Revision 1.1Aug 23, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Light chain from Fab of C10_S66K antibody
L: Light chain from Fab of C10_S66K antibody
B: Heavy chain from Fab of C10_S66K antibody
H: Heavy chain from Fab of C10_S66K antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,1336
Polymers93,4604
Non-polymers6732
Water13,926773
1
A: Light chain from Fab of C10_S66K antibody
B: Heavy chain from Fab of C10_S66K antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0673
Polymers46,7302
Non-polymers3361
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3060 Å2
ΔGint-25 kcal/mol
Surface area19500 Å2
MethodPISA
2
L: Light chain from Fab of C10_S66K antibody
H: Heavy chain from Fab of C10_S66K antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,0673
Polymers46,7302
Non-polymers3361
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-24 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.288, 73.354, 95.197
Angle α, β, γ (deg.)90.00, 90.53, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Light chain from Fab of C10_S66K antibody


Mass: 22898.258 Da / Num. of mol.: 2
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 Heavy chain from Fab of C10_S66K antibody


Mass: 23831.975 Da / Num. of mol.: 2
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-7V7 / N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide


Mass: 336.471 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C22H28N2O / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 773 / 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: 2.66 Å3/Da / Density % sol: 53.81 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1.0 M Li-chloride, 10% PEG-6000, 0.1 M Bicine pH 9.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL12-2 / Wavelength: 0.97946 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 19, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97946 Å / Relative weight: 1
ReflectionResolution: 1.8→50 Å / Num. obs: 87845 / % possible obs: 96.9 % / Redundancy: 3.2 % / CC1/2: 0.946 / Net I/σ(I): 21.1
Reflection shellResolution: 1.8→1.83 Å / Num. unique obs: 4175 / CC1/2: 0.776

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
HKL-2000data reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→34.72 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.36 / Phase error: 20.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2155 4487 5.11 %
Rwork0.1784 --
obs0.1803 87773 96.59 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.8→34.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6303 0 50 773 7126
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0136685
X-RAY DIFFRACTIONf_angle_d1.2739193
X-RAY DIFFRACTIONf_dihedral_angle_d11.13956
X-RAY DIFFRACTIONf_chiral_restr0.0911069
X-RAY DIFFRACTIONf_plane_restr0.0111176
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8-1.820.26811230.21842359X-RAY DIFFRACTION81
1.82-1.840.27171770.22162659X-RAY DIFFRACTION97
1.84-1.870.28051570.21072855X-RAY DIFFRACTION99
1.87-1.890.27751500.19952803X-RAY DIFFRACTION98
1.89-1.910.21841540.19992762X-RAY DIFFRACTION97
1.91-1.940.23911140.19312843X-RAY DIFFRACTION97
1.94-1.970.23691420.18572845X-RAY DIFFRACTION99
1.97-20.22691540.18372770X-RAY DIFFRACTION99
2-2.030.23651310.18772860X-RAY DIFFRACTION98
2.03-2.060.24621330.19052786X-RAY DIFFRACTION98
2.06-2.10.24751790.19742778X-RAY DIFFRACTION97
2.1-2.140.22011880.18622763X-RAY DIFFRACTION99
2.14-2.180.24511800.18052822X-RAY DIFFRACTION98
2.18-2.220.23371480.18232837X-RAY DIFFRACTION99
2.22-2.270.22561690.18862719X-RAY DIFFRACTION97
2.27-2.320.25611480.18022808X-RAY DIFFRACTION98
2.32-2.380.22791300.17622836X-RAY DIFFRACTION98
2.38-2.440.18721080.1812779X-RAY DIFFRACTION96
2.44-2.520.24541500.1812729X-RAY DIFFRACTION95
2.52-2.60.22581630.18522635X-RAY DIFFRACTION93
2.6-2.690.2391690.19172829X-RAY DIFFRACTION98
2.69-2.80.2571730.19272811X-RAY DIFFRACTION99
2.8-2.920.22941300.19052856X-RAY DIFFRACTION98
2.92-3.080.22431410.18532842X-RAY DIFFRACTION98
3.08-3.270.22721230.17832838X-RAY DIFFRACTION97
3.27-3.520.1871420.17152790X-RAY DIFFRACTION96
3.52-3.880.2081440.16042769X-RAY DIFFRACTION96
3.88-4.440.16851690.14622727X-RAY DIFFRACTION95
4.44-5.590.15221470.14472702X-RAY DIFFRACTION93
5.59-34.720.18541510.18552874X-RAY DIFFRACTION96

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