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- PDB-10bt: X-ray Crystal Structure of A High-Affinity Monoclonal Antibody Se... -

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Basic information

Entry
Database: PDB / ID: 10bt
TitleX-ray Crystal Structure of A High-Affinity Monoclonal Antibody Sequesters Xylazine
Components
  • Antibody Heavy Chain
  • Antibody Light Chain
KeywordsIMMUNE SYSTEM / monoclonal antibody
Function / homology:
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.99 Å
AuthorsShi, K. / Moller, N. / Aihara, H.
Funding support United States, 2items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R35-GM118047 United States
National Institutes of Health/National Institute on Drug Abuse (NIH/NIDA)UH3DA048386 United States
CitationJournal: Acs Pharmacol Transl Sci / Year: 2026
Title: Discovery, Structural Characterization, and Preclinical Evaluation of Monoclonal Antibodies against Xylazine Poisoning
Authors: Kang, J. / Xu, R. / Lee, S. / Luengas, D. / Kim, C.M. / Marecki, C. / Gallant, J. / Moeller, N. / Shi, K. / Jahan, R. / Hicks, D. / Runyon, S. / Aihara, H. / Pravetoni, M.
History
DepositionJan 10, 2026Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 10, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Antibody Heavy Chain
B: Antibody Heavy Chain
C: Antibody Heavy Chain
D: Antibody Heavy Chain
E: Antibody Light Chain
F: Antibody Light Chain
G: Antibody Light Chain
H: Antibody Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)197,27416
Polymers196,2508
Non-polymers1,0238
Water16,033890
1
A: Antibody Heavy Chain
E: Antibody Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3184
Polymers49,0632
Non-polymers2562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3570 Å2
ΔGint-37 kcal/mol
Surface area20030 Å2
MethodPISA
2
B: Antibody Heavy Chain
F: Antibody Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3184
Polymers49,0632
Non-polymers2562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3420 Å2
ΔGint-36 kcal/mol
Surface area20170 Å2
MethodPISA
3
C: Antibody Heavy Chain
G: Antibody Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3184
Polymers49,0632
Non-polymers2562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3390 Å2
ΔGint-35 kcal/mol
Surface area19820 Å2
MethodPISA
4
D: Antibody Heavy Chain
H: Antibody Light Chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)49,3184
Polymers49,0632
Non-polymers2562
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3610 Å2
ΔGint-38 kcal/mol
Surface area20400 Å2
MethodPISA
Unit cell
Length a, b, c (Å)89.178, 121.034, 95.621
Angle α, β, γ (deg.)90.00, 112.45, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody
Antibody Heavy Chain


Mass: 25435.330 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody
Antibody Light Chain


Mass: 23627.289 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Chemical
ChemComp-A1C4R / N-(2,6-dimethylphenyl)-5,6-dihydro-4H-1,3-thiazin-2-amine


Mass: 220.334 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C12H16N2S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 890 / 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: 2.43 Å3/Da / Density % sol: 49.39 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop
Details: J002007, F05_10 100 mM Tris base, pH 8, 8 (%w/v) PEG 20000, 100 mM Sodium chloride

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS-II / Beamline: 17-ID-1 / Wavelength: 0.919887 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Dec 13, 2025
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.919887 Å / Relative weight: 1
ReflectionResolution: 1.99→44.187 Å / Num. obs: 68933 / % possible obs: 53.7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.157 / Rpim(I) all: 0.083 / Rrim(I) all: 0.179 / Net I/σ(I): 4.3 / Num. measured all: 310426
Reflection shellResolution: 1.99→2.341 Å / % possible obs: 7 % / Redundancy: 4.5 % / Rmerge(I) obs: 0.849 / Num. measured all: 15433 / Num. unique obs: 3447 / Rpim(I) all: 0.449 / Rrim(I) all: 0.962 / Net I/σ(I) obs: 1.6

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Processing

Software
NameVersionClassification
Aimlessdata scaling
PDB_EXTRACTdata extraction
PHENIXv1.21.2refinement
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.99→41.99 Å / Cross valid method: FREE R-VALUE
RfactorNum. reflection% reflection
Rfree0.2332 3376 4.9 %
Rwork0.1767 --
obs0.1795 68931 53.73 %
Refinement stepCycle: LAST / Resolution: 1.99→41.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms13308 0 64 890 14262
LS refinement shellResolution: 1.99→2.09 Å
RfactorNum. reflection% reflection
Rfree0.3823 21 -
Rwork0.2907 275 -
obs--2 %

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