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- PDB-7u64: Crystal Structure of Anti-Fentanyl Antibody HY6-F9.6 Fab Complexe... -

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Basic information

Entry
Database: PDB / ID: 7u64
TitleCrystal Structure of Anti-Fentanyl Antibody HY6-F9.6 Fab Complexed with Fentanyl
Components(HY6-F9.6 Fab ...) x 2
KeywordsIMMUNE SYSTEM / mAb / opioid
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-7V7 / ACETATE ION
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.75 Å
AuthorsRodarte, J.V. / Pancera, M.P.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)UG3 DA047711 United States
CitationJournal: Structure / Year: 2023
Title: Structures of drug-specific monoclonal antibodies bound to opioids and nicotine reveal a common mode of binding.
Authors: Rodarte, J.V. / Baehr, C. / Hicks, D. / Liban, T.L. / Weidle, C. / Rupert, P.B. / Jahan, R. / Wall, A. / McGuire, A.T. / Strong, R.K. / Runyon, S. / Pravetoni, M. / Pancera, M.
History
DepositionMar 3, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 11, 2023Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2023Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model
Revision 1.3Oct 16, 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: HY6-F9.6 Fab heavy chain
B: HY6-F9.6 Fab light chain
C: HY6-F9.6 Fab heavy chain
D: HY6-F9.6 Fab light chain
E: HY6-F9.6 Fab heavy chain
F: HY6-F9.6 Fab light chain
G: HY6-F9.6 Fab heavy chain
H: HY6-F9.6 Fab light chain
I: HY6-F9.6 Fab heavy chain
J: HY6-F9.6 Fab light chain
K: HY6-F9.6 Fab heavy chain
L: HY6-F9.6 Fab light chain
M: HY6-F9.6 Fab heavy chain
N: HY6-F9.6 Fab light chain
O: HY6-F9.6 Fab heavy chain
P: HY6-F9.6 Fab light chain
Q: HY6-F9.6 Fab heavy chain
R: HY6-F9.6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)441,946100
Polymers435,11318
Non-polymers6,83482
Water50,9642829
1
A: HY6-F9.6 Fab heavy chain
B: HY6-F9.6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,33214
Polymers48,3462
Non-polymers98612
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6130 Å2
ΔGint-37 kcal/mol
Surface area19100 Å2
MethodPISA
2
C: HY6-F9.6 Fab heavy chain
D: HY6-F9.6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,7645
Polymers48,3462
Non-polymers4193
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4190 Å2
ΔGint-38 kcal/mol
Surface area19240 Å2
MethodPISA
3
E: HY6-F9.6 Fab heavy chain
F: HY6-F9.6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,08311
Polymers48,3462
Non-polymers7379
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5040 Å2
ΔGint-39 kcal/mol
Surface area19250 Å2
MethodPISA
4
G: HY6-F9.6 Fab heavy chain
H: HY6-F9.6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,28315
Polymers48,3462
Non-polymers93713
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6070 Å2
ΔGint-57 kcal/mol
Surface area19000 Å2
MethodPISA
5
I: HY6-F9.6 Fab heavy chain
J: HY6-F9.6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,02410
Polymers48,3462
Non-polymers6788
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5150 Å2
ΔGint-56 kcal/mol
Surface area19270 Å2
MethodPISA
6
K: HY6-F9.6 Fab heavy chain
L: HY6-F9.6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,08311
Polymers48,3462
Non-polymers7379
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4990 Å2
ΔGint-35 kcal/mol
Surface area19260 Å2
MethodPISA
7
M: HY6-F9.6 Fab heavy chain
N: HY6-F9.6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,8005
Polymers48,3462
Non-polymers4553
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-28 kcal/mol
Surface area19170 Å2
MethodPISA
8
O: HY6-F9.6 Fab heavy chain
P: HY6-F9.6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,20113
Polymers48,3462
Non-polymers85511
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5370 Å2
ΔGint-47 kcal/mol
Surface area19280 Å2
MethodPISA
9
Q: HY6-F9.6 Fab heavy chain
R: HY6-F9.6 Fab light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,37816
Polymers48,3462
Non-polymers1,03214
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6030 Å2
ΔGint-45 kcal/mol
Surface area19060 Å2
MethodPISA
Unit cell
Length a, b, c (Å)218.139, 218.139, 89.023
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

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Antibody , 2 types, 18 molecules ACEGIKMOQBDFHJLNPR

#1: Antibody
HY6-F9.6 Fab heavy chain


Mass: 24345.039 Da / Num. of mol.: 9
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody
HY6-F9.6 Fab light chain


Mass: 24000.818 Da / Num. of mol.: 9
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 , 4 types, 2911 molecules

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


Mass: 336.471 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: C22H28N2O / Feature type: SUBJECT OF INVESTIGATION / Comment: medication*YM
#4: Chemical...
ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 59 / Source method: isolated from a natural source / Formula: C2H3O2
#5: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 14 / Source method: isolated from a natural source / Formula: Na
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2829 / 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: 2.86 Å3/Da / Density % sol: 56.94 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 2.8M Sodium Acetate

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.97388 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 28, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97388 Å / Relative weight: 1
ReflectionResolution: 1.75→43.33 Å / Num. obs: 475987 / % possible obs: 99.6 % / Redundancy: 5.1 % / Biso Wilson estimate: 16.94 Å2 / CC1/2: 0.994 / Rpim(I) all: 0.068 / Rrim(I) all: 0.155 / Net I/σ(I): 7.7
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Mean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
1.75-1.7851.3234820.7890.4420.99898.8
9.59-43.335.328.428820.9990.020.04798.9

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4LEX

4lex


Resolution: 1.75→43.33 Å / SU ML: 0.1994 / Cross valid method: FREE R-VALUE / σ(F): 1.96 / Phase error: 26.933
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2249 23982 5.04 %
Rwork0.1972 451470 -
obs0.1986 475452 99.49 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 23.94 Å2
Refinement stepCycle: LAST / Resolution: 1.75→43.33 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms30132 0 475 2829 33436
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.006331263
X-RAY DIFFRACTIONf_angle_d0.896242486
X-RAY DIFFRACTIONf_chiral_restr0.0584770
X-RAY DIFFRACTIONf_plane_restr0.00665414
X-RAY DIFFRACTIONf_dihedral_angle_d13.764911097
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.75-1.770.31158110.283815101X-RAY DIFFRACTION99.19
1.77-1.790.31248530.272614841X-RAY DIFFRACTION98.77
1.79-1.810.29287900.259514901X-RAY DIFFRACTION98.72
1.81-1.840.27747240.252615072X-RAY DIFFRACTION99.54
1.84-1.860.30538040.245814960X-RAY DIFFRACTION98.58
1.86-1.890.26758360.244115032X-RAY DIFFRACTION99.52
1.89-1.910.2648340.239114984X-RAY DIFFRACTION99.21
1.91-1.940.29177460.238414995X-RAY DIFFRACTION98.99
1.94-1.970.2517810.219715170X-RAY DIFFRACTION99.58
1.97-20.23857480.204414930X-RAY DIFFRACTION99.39
2-2.040.24678680.214985X-RAY DIFFRACTION99.22
2.04-2.070.24897360.21415111X-RAY DIFFRACTION99.3
2.07-2.110.25097850.198815069X-RAY DIFFRACTION99.69
2.11-2.160.21988010.189815018X-RAY DIFFRACTION99.7
2.16-2.20.21198510.189515084X-RAY DIFFRACTION99.51
2.2-2.260.23288100.195815028X-RAY DIFFRACTION99.6
2.26-2.310.23467880.187515052X-RAY DIFFRACTION99.65
2.31-2.380.22418140.189715044X-RAY DIFFRACTION99.65
2.38-2.440.23258600.190415070X-RAY DIFFRACTION99.61
2.44-2.520.23997650.198215003X-RAY DIFFRACTION99.6
2.52-2.610.2477300.201815290X-RAY DIFFRACTION99.86
2.61-2.720.24188880.20514982X-RAY DIFFRACTION99.78
2.72-2.840.24227190.203415217X-RAY DIFFRACTION99.93
2.84-2.990.22237600.199915093X-RAY DIFFRACTION99.88
2.99-3.180.22298470.193115123X-RAY DIFFRACTION99.85
3.18-3.420.20357920.179415112X-RAY DIFFRACTION99.84
3.43-3.770.18528240.164215063X-RAY DIFFRACTION99.96
3.77-4.310.16828210.159215060X-RAY DIFFRACTION99.89
4.31-5.430.16988140.160715076X-RAY DIFFRACTION99.49
5.43-43.330.23487820.219815004X-RAY DIFFRACTION99.11

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