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- PDB-8tfp: Fab from C10-S66K antibody in complex with carfentanil -

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Basic information

Entry
Database: PDB / ID: 8tfp
TitleFab from C10-S66K antibody in complex with carfentanil
Components
  • Heavy chain of Fab from C10-S66K antibody
  • Light chain of Fab from C10-S66K antibody
KeywordsIMMUNE SYSTEM / Antibody / fentanyl analogue / carfentanil / opioid.
Function / homologyCarfentanil
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.78 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 1.2Sep 20, 2023Group: Derived calculations / Structure summary / Category: chem_comp / entity / pdbx_entity_nonpoly
Item: _chem_comp.name / _chem_comp.pdbx_synonyms ..._chem_comp.name / _chem_comp.pdbx_synonyms / _entity.pdbx_description / _pdbx_entity_nonpoly.name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Light chain of Fab from C10-S66K antibody
L: Light chain of Fab from C10-S66K antibody
B: Heavy chain of Fab from C10-S66K antibody
H: Heavy chain of Fab from C10-S66K antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,2496
Polymers93,4604
Non-polymers7892
Water14,520806
1
A: Light chain of Fab from C10-S66K antibody
B: Heavy chain of Fab from C10-S66K antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1253
Polymers46,7302
Non-polymers3951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3220 Å2
ΔGint-24 kcal/mol
Surface area19040 Å2
MethodPISA
2
L: Light chain of Fab from C10-S66K antibody
H: Heavy chain of Fab from C10-S66K antibody
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,1253
Polymers46,7302
Non-polymers3951
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3370 Å2
ΔGint-25 kcal/mol
Surface area19150 Å2
MethodPISA
Unit cell
Length a, b, c (Å)71.050, 73.492, 95.089
Angle α, β, γ (deg.)90.00, 90.38, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody Light chain of Fab from 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 of Fab from 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-84K / Carfentanil / methyl 1-(2-phenylethyl)-4-(N-phenylpropanamido)piperidine-4-carboxylate


Mass: 394.507 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H30N2O3 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 806 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 53.69 %
Crystal growTemperature: 293.15 K / Method: vapor diffusion, sitting drop
Details: 1.0 M Li-chloride, 10% PEG-6000, 0.1 M HEPES pH 7.0

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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: 1.78→95.09 Å / Num. obs: 91341 / % possible obs: 97.8 % / Redundancy: 3.2 % / CC1/2: 0.965 / Net I/σ(I): 6.5
Reflection shellResolution: 1.78→1.81 Å / Num. unique obs: 4542 / CC1/2: 0.862

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.78→34.72 Å / SU ML: 0.17 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 19.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2071 2001 2.19 %
Rwork0.1782 --
obs0.1789 91258 97.54 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.78→34.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6296 0 58 806 7160
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0056689
X-RAY DIFFRACTIONf_angle_d0.8919200
X-RAY DIFFRACTIONf_dihedral_angle_d6.98957
X-RAY DIFFRACTIONf_chiral_restr0.0581068
X-RAY DIFFRACTIONf_plane_restr0.0071175
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.78-1.830.24091340.196407X-RAY DIFFRACTION98
1.83-1.880.24461320.17976401X-RAY DIFFRACTION98
1.88-1.930.20391440.17526382X-RAY DIFFRACTION98
1.93-1.990.22451450.17446330X-RAY DIFFRACTION98
1.99-2.060.19991520.17896242X-RAY DIFFRACTION96
2.06-2.150.20751310.18296125X-RAY DIFFRACTION94
2.15-2.250.22811400.18466309X-RAY DIFFRACTION97
2.25-2.360.22741570.18486509X-RAY DIFFRACTION99
2.36-2.510.251410.19066435X-RAY DIFFRACTION99
2.51-2.710.22731460.19996436X-RAY DIFFRACTION98
2.71-2.980.21781440.19336364X-RAY DIFFRACTION97
2.98-3.410.21621430.18346280X-RAY DIFFRACTION96
3.41-4.290.17651440.16046540X-RAY DIFFRACTION99
4.29-34.720.1761480.1656497X-RAY DIFFRACTION97
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)
10.0923-0.07190.05430.0853-0.01620.07590.0147-0.07230.0555-0.01620.05230.02050.0482-0.0970.01630.05930.0021-0.00260.11310.02720.0811-57.664-3.696-62.486
20.0034-0.0024-0.0010.0016-0.00040.00090.0633-0.0408-0.0259-0.0123-0.0085-0.1110.0258-0.030900.1285-0.01910.01630.29870.00530.1447-67.945-0.868-43.771
30.11230.0269-0.10020.0635-0.0570.0923-0.00150.01810.1994-0.0310.12860.0639-0.0079-0.03150.00740.0921-0.0181-0.00690.1545-0.00560.1413-58.9015.439-21.934
40.06650.0339-0.08320.0538-0.00810.10660.0266-0.0207-0.0588-0.0026-0.02340.0082-0.0441-0.1041-0.00840.08950.00910.00070.12840.00620.055-24.1530.27216.237
50.03820.0240.03460.030.00760.03240.05450.00310.0384-0.0230.0054-0.04450.0193-0.00510.00070.09140.01510.00710.1552-0.01390.0987-22.286-7.266-18.627
60.10390.01740.01550.0395-0.03810.03520.0565-0.031-0.08490.030.098-0.03670.0925-0.00250.00160.14030.00810.00640.1464-0.01810.0901-25.667-12.37-21.3
70.06720.004-0.0180.0047-0.00330.02420.0758-0.088-0.0445-0.0044-0.03970.02380.04450.04360.00220.102-0.00560.0090.0653-0.01680.1078-34.831-12.407-53.232
80.05720.03820.03510.02950.0050.04690.0436-0.00270.0224-0.0167-0.0481-0.054-0.0175-0.032200.06870.01680.01150.0412-0.00930.0716-34.836-6.414-59.743
90.056-0.06640.00060.06060.00310.00880.0750.0285-0.0217-0.0270.0164-0.0686-0.0566-0.0140.00040.0742-0.00980.00410.0559-0.01550.0703-39.984-4.146-52.404
100.0269-0.011-0.01410.01660.02840.0459-0.0233-0.0023-0.0182-0.0023-0.01350.1310.0566-0.067-0.04860.0796-0.17370.0672-0.11510.09070.1112-50.264-5.21-26.202
110.02510.02650.01020.04130.03770.065-0.023-0.0825-0.1154-0.02290.05270.038-0.02940.02490.02230.12790.00630.02760.09630.07020.1235-43.403-10.557-23.178
120.03220.00410.01860.0064-0.00750.02220.01060.0770.01340.0221-0.04750.0449-0.03860.0854-0.00060.13060.0057-0.00110.0778-0.01850.1044-0.0484.2846.472
130.1032-0.0344-00.03930.00090.09670.0419-0.0492-0.03660.0261-0.0522-0.02540.0051-0.0236-00.0625-0.0041-0.01130.045-0.00570.0648-3.2850.30412.828
140.08270.0287-0.02910.05870.00720.0648-0.02120.1270.0760.015-0.00140.0519-0.0179-0.00840.00180.12260.0388-0.04170.10820.01340.1341-12.115-0.483-18.82
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1( CHAIN A AND RESID 3:102 )A3 - 102
2X-RAY DIFFRACTION2( CHAIN A AND RESID 103:115 )A103 - 115
3X-RAY DIFFRACTION3( CHAIN A AND RESID 116:209 )A116 - 209
4X-RAY DIFFRACTION4( CHAIN L AND RESID 3:102 )L3 - 102
5X-RAY DIFFRACTION5( CHAIN L AND RESID 103:139 )L103 - 139
6X-RAY DIFFRACTION6( CHAIN L AND RESID 140:209 )L140 - 209
7X-RAY DIFFRACTION7( CHAIN B AND RESID 1:33 )B1 - 33
8X-RAY DIFFRACTION8( CHAIN B AND RESID 34:83 )B34 - 83
9X-RAY DIFFRACTION9( CHAIN B AND RESID 84:125 )B84 - 125
10X-RAY DIFFRACTION10( CHAIN B AND RESID 131:195 )B131 - 195
11X-RAY DIFFRACTION11( CHAIN B AND RESID 196:212 )B196 - 212
12X-RAY DIFFRACTION12( CHAIN H AND RESID 2:33 )H2 - 33
13X-RAY DIFFRACTION13( CHAIN H AND RESID 34:117 )H34 - 117
14X-RAY DIFFRACTION14( CHAIN H AND RESID 118:213 )H118 - 213

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