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- PDB-9fyt: mAbs in complex with cobratoxin at pH 4.5 -

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Basic information

Entry
Database: PDB / ID: 9fyt
TitlemAbs in complex with cobratoxin at pH 4.5
Components
  • Alpha-cobratoxin
  • Light chain scFv A01
  • heavy chain scFv Ao1
KeywordsTOXIN / mAbs / cobratoxin / antibody:toxin complex
Function / homology
Function and homology information


acetylcholine receptor inhibitor activity / ion channel regulator activity / toxin activity / extracellular region
Similarity search - Function
Snake toxin, conserved site / Snake toxins signature. / : / Snake toxin cobra-type / Snake three-finger toxin / Snake toxin-like superfamily
Similarity search - Domain/homology
Biological speciesNaja kaouthia (monocled cobra)
Homo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.55 Å
AuthorsWade, J. / Bohn, M.F. / Laustsen, A.H. / Morth, J.P.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Research Council (ERC)European Union
CitationJournal: To Be Published
Title: Structural mechanisms of a-neurotoxin-neutralizing antibodies enable rational design of pH-dependent antigen binding
Authors: wade, J.
History
DepositionJul 3, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 16, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha-cobratoxin
B: Alpha-cobratoxin
I: Light chain scFv A01
M: heavy chain scFv Ao1
C: Light chain scFv A01
D: heavy chain scFv Ao1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)71,38117
Polymers70,6726
Non-polymers70911
Water9,386521
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9360 Å2
ΔGint-96 kcal/mol
Surface area28920 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.860, 83.860, 98.650
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Alpha-cobratoxin / Alpha-CT / Alpha-CbT / Alpha-Cbtx / Alpha-Ctx / Alpha-elapitoxin-Nk2a / Alpha-EPTX-Nk2a / Long ...Alpha-CT / Alpha-CbT / Alpha-Cbtx / Alpha-Ctx / Alpha-elapitoxin-Nk2a / Alpha-EPTX-Nk2a / Long neurotoxin 1 / Siamensis 3


Mass: 7842.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Naja kaouthia (monocled cobra) / Production host: Naja kaouthia (monocled cobra) / References: UniProt: P01391

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Antibody , 2 types, 4 molecules ICMD

#2: Antibody Light chain scFv A01


Mass: 15073.576 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)
#3: Antibody heavy chain scFv Ao1


Mass: 12420.419 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli)

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Non-polymers , 5 types, 532 molecules

#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#5: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C3H8O3
#6: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 521 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.25 Å3/Da / Density % sol: 45.32 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 4.5
Details: 0.1 M Bis-Tris pH 6.5, 0.2 M Ammonium Sulfate, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 24, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.55→42.52 Å / Num. obs: 92830 / % possible obs: 99.64 % / Redundancy: 5.2 % / Biso Wilson estimate: 21.44 Å2 / CC1/2: 0.999 / Net I/σ(I): 10.86
Reflection shellResolution: 1.55→1.605 Å / Num. unique obs: 9112 / CC1/2: 0.69

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Processing

Software
NameVersionClassification
PHENIX1.20.1_4487refinement
xia2data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.55→42.52 Å / SU ML: 0.2537 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 32.2916
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2373 8834 4.98 %
Rwork0.1855 168708 -
obs0.1881 88771 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 33.8 Å2
Refinement stepCycle: LAST / Resolution: 1.55→42.52 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4794 0 40 521 5355
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.00945049
X-RAY DIFFRACTIONf_angle_d1.02386877
X-RAY DIFFRACTIONf_chiral_restr0.0647743
X-RAY DIFFRACTIONf_plane_restr0.0092899
X-RAY DIFFRACTIONf_dihedral_angle_d7.3185730
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.55-1.570.4483050.44465359X-RAY DIFFRACTION95.29
1.57-1.590.45793060.42915612X-RAY DIFFRACTION99.33
1.59-1.610.43692860.39845654X-RAY DIFFRACTION99.3
1.61-1.630.38862490.3835647X-RAY DIFFRACTION99.44
1.63-1.650.38162720.36365695X-RAY DIFFRACTION99.6
1.65-1.670.40833300.34335598X-RAY DIFFRACTION99.65
1.67-1.690.37383020.32915618X-RAY DIFFRACTION99.78
1.69-1.720.36932870.30445664X-RAY DIFFRACTION99.5
1.72-1.750.33643210.28265647X-RAY DIFFRACTION99.58
1.75-1.770.322680.2765646X-RAY DIFFRACTION99.7
1.77-1.80.31362770.25735626X-RAY DIFFRACTION99.39
1.8-1.840.28712990.2555682X-RAY DIFFRACTION99.58
1.84-1.870.30243160.23615574X-RAY DIFFRACTION99.7
1.87-1.910.29953430.22365619X-RAY DIFFRACTION99.5
1.91-1.950.29092870.20385628X-RAY DIFFRACTION99.34
1.95-20.24883210.18245619X-RAY DIFFRACTION99.7
2-2.050.26232780.18775668X-RAY DIFFRACTION99.63
2.05-2.10.25673010.1795580X-RAY DIFFRACTION99.59
2.1-2.170.20962710.16835682X-RAY DIFFRACTION99.43
2.17-2.240.24732760.16865666X-RAY DIFFRACTION99.17
2.24-2.320.23892670.17045682X-RAY DIFFRACTION99.61
2.32-2.410.2252680.16345637X-RAY DIFFRACTION99.68
2.41-2.520.23632900.16195609X-RAY DIFFRACTION99.51
2.52-2.650.21043030.17075683X-RAY DIFFRACTION99.27
2.65-2.820.21242910.1775602X-RAY DIFFRACTION99.38
2.82-3.030.24882990.17715584X-RAY DIFFRACTION99.12
3.03-3.340.25062340.16865698X-RAY DIFFRACTION99.02
3.34-3.820.21084040.1495513X-RAY DIFFRACTION99.46
3.82-4.810.15762800.12285632X-RAY DIFFRACTION99.38
4.81-42.520.17693030.15725584X-RAY DIFFRACTION98.69

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