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- PDB-7u63: Crystal Structure Anti-Oxycodone Antibody HY2-A12 Fab Complexed w... -

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Basic information

Entry
Database: PDB / ID: 7u63
TitleCrystal Structure Anti-Oxycodone Antibody HY2-A12 Fab Complexed with Oxycodone
Components
  • HY2-A12 Fab Heavy Chain
  • HY2-A12 Fab Light Chain
KeywordsIMMUNE SYSTEM / mAb / opioid
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-OOX
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsRodarte, J.V. / Pancera, M.P. / Weidle, C. / Rupert, P.B. / Strong, R.K.
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 1.3Nov 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

Downloads & links

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Assembly

Deposited unit
L: HY2-A12 Fab Light Chain
H: HY2-A12 Fab Heavy Chain
A: HY2-A12 Fab Light Chain
B: HY2-A12 Fab Heavy Chain
C: HY2-A12 Fab Light Chain
D: HY2-A12 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)142,0379
Polymers141,0906
Non-polymers9463
Water4,306239
1
L: HY2-A12 Fab Light Chain
H: HY2-A12 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3463
Polymers47,0302
Non-polymers3151
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3580 Å2
ΔGint-29 kcal/mol
Surface area18170 Å2
MethodPISA
2
A: HY2-A12 Fab Light Chain
B: HY2-A12 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3463
Polymers47,0302
Non-polymers3151
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-29 kcal/mol
Surface area18500 Å2
MethodPISA
3
C: HY2-A12 Fab Light Chain
D: HY2-A12 Fab Heavy Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,3463
Polymers47,0302
Non-polymers3151
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-29 kcal/mol
Surface area18650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.624, 67.989, 85.623
Angle α, β, γ (deg.)69.130, 67.600, 68.640
Int Tables number1
Space group name H-MP1

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Components

#1: Antibody HY2-A12 Fab Light Chain


Mass: 23042.525 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#2: Antibody HY2-A12 Fab Heavy Chain


Mass: 23987.631 Da / Num. of mol.: 3 / Source method: isolated from a natural source / Source: (natural) Mus musculus (house mouse)
#3: Chemical ChemComp-OOX / 14-hydroxy-3-methoxy-17-methyl-5beta-4,5-epoxymorphinan-6-one / Oxycodone


Mass: 315.364 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C18H21NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.32 Å3/Da / Density % sol: 47.09 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / Details: Tris pH 8.5, 0.1M 20% PEG 3350 Isopropanol 20%

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Data collection

DiffractionMean temperature: 80 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 19, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.24→50 Å / Num. obs: 59023 / % possible obs: 97.4 % / Redundancy: 1.8 % / Biso Wilson estimate: 28.8 Å2 / Rmerge(I) obs: 0.034 / Rpim(I) all: 0.034 / Rrim(I) all: 0.049 / Χ2: 0.889 / Net I/σ(I): 14.4 / Num. measured all: 103835
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.24-2.281.60.38328980.7160.3830.5421.06296.6
2.28-2.321.70.36529500.750.3650.5170.94296.3
2.32-2.361.70.30829180.8040.3080.4360.94797
2.36-2.411.80.27529790.8350.2750.3890.97897.3
2.41-2.471.80.23329050.8750.2330.3290.96997.1
2.47-2.521.80.20829740.8890.2080.2951.00797.3
2.52-2.591.80.16529620.9310.1650.2330.97697.4
2.59-2.661.80.12829000.9530.1280.1820.95297.2
2.66-2.731.70.129670.9720.10.1410.94897.4
2.73-2.821.70.07829730.9830.0780.1110.95696.7
2.82-2.921.70.0629330.9890.060.0850.91797.6
2.92-3.041.80.0529640.9920.050.0710.997.5
3.04-3.181.80.03829490.9940.0380.0540.83897.4
3.18-3.351.80.03229520.9960.0320.0450.8498
3.35-3.561.70.02629500.9960.0260.0370.76797.2
3.56-3.831.70.02629570.9960.0260.0370.83897.7
3.83-4.221.80.02530150.9960.0250.0360.7398.5
4.22-4.821.80.02529650.9960.0250.0350.72898.2
4.82-6.081.70.02629790.9950.0260.0370.71598.6
6.08-501.80.0329330.9970.030.0420.82397.1

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Processing

Software
NameVersionClassification
PHENIX1.19.2_4158refinement
SCALEPACKdata scaling
PDB_EXTRACT3.27data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3TT1

3tt1


Resolution: 2.3→42.85 Å / SU ML: 0.31 / Cross valid method: THROUGHOUT / σ(F): 1.98 / Phase error: 31.04 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2822 2633 5.03 %
Rwork0.2257 49712 -
obs0.2285 52345 92.68 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 106.93 Å2 / Biso mean: 35.5981 Å2 / Biso min: 5.97 Å2
Refinement stepCycle: final / Resolution: 2.3→42.85 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9304 0 69 239 9612
Biso mean--34.25 26.78 -
Num. residues----1258
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / Total num. of bins used: 19

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.3-2.340.3505940.2871732182661
2.34-2.390.33581040.27681917202168
2.39-2.440.35371330.27342313244682
2.44-2.490.31581230.27182530265390
2.49-2.550.32391510.27422700285195
2.55-2.610.35721260.26642764289097
2.61-2.680.38191350.26172718285397
2.68-2.760.30181390.25692783292298
2.76-2.850.30951490.25632729287897
2.85-2.950.3121570.25662764292198
2.95-3.070.33491600.25022735289598
3.07-3.210.3451450.25222731287697
3.21-3.380.30991590.24282725288498
3.38-3.590.26711490.21832752290197
3.59-3.870.25291420.2162755289798
3.87-4.250.25311550.18822792294798
4.25-4.870.19271390.17152777291698
4.87-6.130.23761640.18882755291999
6.13-42.850.24141090.20712740284996

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