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- PDB-9axn: Crystal Structure of Anti-Fentanyl Antibody HY11-6B2_Mu Fab in Co... -

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Basic information

Entry
Database: PDB / ID: 9axn
TitleCrystal Structure of Anti-Fentanyl Antibody HY11-6B2_Mu Fab in Complex with Fentanyl
Components(HY11-6B2_Mu Fab ...) x 2
KeywordsIMMUNE SYSTEM / opioids / mAb / fentanyl
Function / homologyChem-7V7 / NICKEL (II) ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.4 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 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
H: HY11-6B2_Mu Fab Heavy Chain
L: HY11-6B2_Mu Fab Light Chain
A: HY11-6B2_Mu Fab Heavy Chain
C: HY11-6B2_Mu Fab Heavy Chain
D: HY11-6B2_Mu Fab Light Chain
B: HY11-6B2_Mu Fab Light Chain
E: HY11-6B2_Mu Fab Heavy Chain
F: HY11-6B2_Mu Fab Light Chain
J: HY11-6B2_Mu Fab Light Chain
I: HY11-6B2_Mu Fab Heavy Chain
M: HY11-6B2_Mu Fab Heavy Chain
N: HY11-6B2_Mu Fab Light Chain
O: HY11-6B2_Mu Fab Heavy Chain
P: HY11-6B2_Mu Fab Light Chain
Q: HY11-6B2_Mu Fab Heavy Chain
R: HY11-6B2_Mu Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)389,83161
Polymers384,06816
Non-polymers5,76345
Water15,781876
1
H: HY11-6B2_Mu Fab Heavy Chain
L: HY11-6B2_Mu Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7578
Polymers48,0082
Non-polymers7496
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4070 Å2
ΔGint-52 kcal/mol
Surface area19500 Å2
MethodPISA
2
A: HY11-6B2_Mu Fab Heavy Chain
B: HY11-6B2_Mu Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5966
Polymers48,0082
Non-polymers5874
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
ΔGint-51 kcal/mol
Surface area19120 Å2
MethodPISA
3
C: HY11-6B2_Mu Fab Heavy Chain
D: HY11-6B2_Mu Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7888
Polymers48,0082
Non-polymers7796
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4060 Å2
ΔGint-75 kcal/mol
Surface area18990 Å2
MethodPISA
4
E: HY11-6B2_Mu Fab Heavy Chain
F: HY11-6B2_Mu Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8199
Polymers48,0082
Non-polymers8117
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4740 Å2
ΔGint-45 kcal/mol
Surface area19010 Å2
MethodPISA
5
J: HY11-6B2_Mu Fab Light Chain
I: HY11-6B2_Mu Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8199
Polymers48,0082
Non-polymers8117
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4090 Å2
ΔGint-59 kcal/mol
Surface area18880 Å2
MethodPISA
6
M: HY11-6B2_Mu Fab Heavy Chain
N: HY11-6B2_Mu Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,01111
Polymers48,0082
Non-polymers1,0039
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4420 Å2
ΔGint-92 kcal/mol
Surface area19070 Å2
MethodPISA
7
O: HY11-6B2_Mu Fab Heavy Chain
P: HY11-6B2_Mu Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5375
Polymers48,0082
Non-polymers5293
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-47 kcal/mol
Surface area19310 Å2
MethodPISA
8
Q: HY11-6B2_Mu Fab Heavy Chain
R: HY11-6B2_Mu Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5035
Polymers48,0082
Non-polymers4953
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3850 Å2
ΔGint-34 kcal/mol
Surface area19250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.777, 98.238, 159.724
Angle α, β, γ (deg.)77.730, 85.320, 77.950
Int Tables number1
Space group name H-MP1
Space group name HallP1

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Components

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Antibody , 2 types, 16 molecules HACEIMOQLDBFJNPR

#1: Antibody
HY11-6B2_Mu Fab Heavy Chain


Mass: 24508.436 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody
HY11-6B2_Mu Fab Light Chain


Mass: 23500.006 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)

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Non-polymers , 5 types, 921 molecules

#3: Chemical
ChemComp-7V7 / N-phenyl-N-[1-(2-phenylethyl)piperidin-4-yl]propanamide


Mass: 336.471 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C22H28N2O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Chemical...
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 23 / Source method: obtained synthetically / Formula: SO4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-NI / NICKEL (II) ION


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni
#7: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 876 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.83 Å3/Da / Density % sol: 56.57 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 23% PEG 3350, 0.24M 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: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jul 2, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.4→49.37 Å / Num. obs: 154677 / % possible obs: 97.7 % / Redundancy: 1.8 % / Biso Wilson estimate: 35 Å2 / CC1/2: 0.989 / Rmerge(I) obs: 0.106 / Rpim(I) all: 0.106 / Rrim(I) all: 0.151 / Χ2: 1 / Net I/σ(I): 5.8 / Num. measured all: 277415
Reflection shellResolution: 2.4→2.44 Å / % possible obs: 96.4 % / Redundancy: 1.8 % / Rmerge(I) obs: 0.738 / Num. measured all: 13230 / Num. unique obs: 7517 / CC1/2: 0.41 / Rpim(I) all: 0.738 / Rrim(I) all: 1.044 / Χ2: 0.99 / Net I/σ(I) obs: 1

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
HKL-3000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→49.37 Å / SU ML: 0.3283 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 28.8759
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2627 7794 5.04 %
Rwork0.2235 146750 -
obs0.2255 154545 97.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 38.77 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.37 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms25823 0 365 876 27064
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.003326782
X-RAY DIFFRACTIONf_angle_d0.697436395
X-RAY DIFFRACTIONf_chiral_restr0.04674036
X-RAY DIFFRACTIONf_plane_restr0.00514608
X-RAY DIFFRACTIONf_dihedral_angle_d8.69043710
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.430.37032660.33354749X-RAY DIFFRACTION96.55
2.43-2.460.36862440.32394835X-RAY DIFFRACTION95.31
2.46-2.490.34472880.30794825X-RAY DIFFRACTION96.65
2.49-2.520.35062450.2984823X-RAY DIFFRACTION96.46
2.52-2.550.34212540.30084879X-RAY DIFFRACTION97.53
2.55-2.590.32912720.29244935X-RAY DIFFRACTION97.02
2.59-2.620.32042570.29044833X-RAY DIFFRACTION98.26
2.62-2.660.33592690.2844886X-RAY DIFFRACTION96.88
2.66-2.70.35112440.27684906X-RAY DIFFRACTION97.8
2.7-2.750.31172470.27974892X-RAY DIFFRACTION97.57
2.75-2.790.33662500.28114915X-RAY DIFFRACTION97.34
2.79-2.850.34662380.27994919X-RAY DIFFRACTION97.95
2.85-2.90.34072370.28114945X-RAY DIFFRACTION97.48
2.9-2.960.30812700.26544797X-RAY DIFFRACTION97.33
2.96-3.020.30312510.24534892X-RAY DIFFRACTION97.04
3.02-3.090.27782300.24054901X-RAY DIFFRACTION97.92
3.09-3.170.27262560.23144982X-RAY DIFFRACTION97.61
3.17-3.260.26872830.2344887X-RAY DIFFRACTION98.29
3.26-3.350.26322840.22574854X-RAY DIFFRACTION98.2
3.35-3.460.27012780.22474942X-RAY DIFFRACTION97.94
3.46-3.580.24222470.21374887X-RAY DIFFRACTION97.87
3.58-3.730.26592650.20744922X-RAY DIFFRACTION97.78
3.73-3.90.24552720.20484892X-RAY DIFFRACTION97.9
3.9-4.10.23862550.18454950X-RAY DIFFRACTION98.06
4.1-4.360.20222680.17474901X-RAY DIFFRACTION98.14
4.36-4.70.20052930.16254921X-RAY DIFFRACTION98.54
4.7-5.170.17652280.1694958X-RAY DIFFRACTION98.86
5.17-5.920.20662640.18954934X-RAY DIFFRACTION98.62
5.92-7.450.26722810.21684907X-RAY DIFFRACTION98.54
7.45-49.370.21282580.18464881X-RAY DIFFRACTION97.04

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