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- PDB-9axp: Crystal Structure of HY11-7E1_Hu3 Fab in Complex with Carfentanil -

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Basic information

Entry
Database: PDB / ID: 9axp
TitleCrystal Structure of HY11-7E1_Hu3 Fab in Complex with Carfentanil
Components
  • HY11-7E1_Hu3 Fab Heavy Chain
  • HY11-7E1_Hu3 Fab Light Chain
KeywordsIMMUNE SYSTEM / opioids / mAb / carfentanil / cross-reactive
Function / homology: / ACETATE 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 16, 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

Downloads & links

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Assembly

Deposited unit
A: HY11-7E1_Hu3 Fab Heavy Chain
B: HY11-7E1_Hu3 Fab Light Chain
H: HY11-7E1_Hu3 Fab Heavy Chain
L: HY11-7E1_Hu3 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,4308
Polymers95,5034
Non-polymers9274
Water4,216234
1
A: HY11-7E1_Hu3 Fab Heavy Chain
B: HY11-7E1_Hu3 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2154
Polymers47,7512
Non-polymers4642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
ΔGint-24 kcal/mol
Surface area19510 Å2
MethodPISA
2
H: HY11-7E1_Hu3 Fab Heavy Chain
L: HY11-7E1_Hu3 Fab Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,2154
Polymers47,7512
Non-polymers4642
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-23 kcal/mol
Surface area19080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.162, 154.893, 159.760
Angle α, β, γ (deg.)90.000, 90.630, 90.000
Int Tables number5
Space group name H-MI121
Space group name HallC2y(x,y,-x+z)
Components on special symmetry positions
IDModelComponents
11B-334-

HOH

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Components

#1: Antibody HY11-7E1_Hu3 Fab Heavy Chain


Mass: 24372.361 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#2: Antibody HY11-7E1_Hu3 Fab Light Chain


Mass: 23378.889 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse) / Production host: Homo sapiens (human)
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-A1AH7 / methyl 1-{3-[(2-aminoethyl)amino]-3-oxopropyl}-4-(N-phenylpropanamido)piperidine-4-carboxylate


Mass: 404.503 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H32N4O4 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 234 / 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: 2.99 Å3/Da / Density % sol: 58.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M sodium acetate pH 4.6, 2M ammonium sulfate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 0.97741 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Dec 22, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97741 Å / Relative weight: 1
ReflectionResolution: 2.4→49.13 Å / Num. obs: 43457 / % possible obs: 99.2 % / Redundancy: 3.4 % / Biso Wilson estimate: 45.76 Å2 / CC1/2: 0.992 / Rmerge(I) obs: 0.099 / Rpim(I) all: 0.064 / Rrim(I) all: 0.118 / Χ2: 1 / Net I/σ(I): 9 / Num. measured all: 145927
Reflection shellResolution: 2.4→2.49 Å / % possible obs: 100 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.861 / Num. measured all: 15887 / Num. unique obs: 4584 / CC1/2: 0.656 / Rpim(I) all: 0.538 / Rrim(I) all: 1.017 / Χ2: 0.72 / Net I/σ(I) obs: 1.4

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.4→49.13 Å / SU ML: 0.3528 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.2195
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2647 2271 5.23 %
Rwork0.2313 41119 -
obs0.233 43390 99.04 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 63.3 Å2
Refinement stepCycle: LAST / Resolution: 2.4→49.13 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6278 0 66 234 6578
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00346491
X-RAY DIFFRACTIONf_angle_d0.70258842
X-RAY DIFFRACTIONf_chiral_restr0.0472997
X-RAY DIFFRACTIONf_plane_restr0.00541126
X-RAY DIFFRACTIONf_dihedral_angle_d6.0867917
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.4-2.450.3251700.33452580X-RAY DIFFRACTION99.78
2.45-2.510.34061420.31552570X-RAY DIFFRACTION99.78
2.51-2.570.28721440.31042617X-RAY DIFFRACTION99.78
2.57-2.640.32531340.31252541X-RAY DIFFRACTION99.41
2.64-2.720.34811580.32382571X-RAY DIFFRACTION98.95
2.72-2.810.33341500.30682494X-RAY DIFFRACTION98.4
2.81-2.910.36441430.29912615X-RAY DIFFRACTION99.24
2.91-3.020.31571650.27612499X-RAY DIFFRACTION99.7
3.02-3.160.27741230.25362628X-RAY DIFFRACTION99.6
3.16-3.330.34961070.24722625X-RAY DIFFRACTION99.85
3.33-3.540.31591520.24882544X-RAY DIFFRACTION98.11
3.54-3.810.26511210.2352514X-RAY DIFFRACTION96.91
3.81-4.190.25541400.20282551X-RAY DIFFRACTION97.82
4.19-4.80.20781380.17182544X-RAY DIFFRACTION99.08
4.8-6.040.19681150.18382635X-RAY DIFFRACTION99.49
6.05-49.130.19931690.19482591X-RAY DIFFRACTION98.78

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