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- PDB-4jn1: An Antidote for Dabigatran -

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Basic information

Entry
Database: PDB / ID: 4jn1
TitleAn Antidote for Dabigatran
Components
  • anti-dabigatran Fab1, heavy chain
  • anti-dabigatran Fab1, light chain
KeywordsIMMUNE SYSTEM / IgG fragment binding dabigatran
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.89 Å
AuthorsSchiele, F. / Nar, H.
CitationJournal: Blood / Year: 2013
Title: A specific antidote for dabigatran: functional and structural characterization.
Authors: Schiele, F. / van Ryn, J. / Canada, K. / Newsome, C. / Sepulveda, E. / Park, J. / Nar, H. / Litzenburger, T.
History
DepositionMar 14, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 27, 2013Provider: repository / Type: Initial release
Revision 1.1Jul 24, 2013Group: Database references
Revision 1.2Oct 16, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
H: anti-dabigatran Fab1, heavy chain
L: anti-dabigatran Fab1, light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,57310
Polymers47,8372
Non-polymers7378
Water6,593366
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5870 Å2
ΔGint-28 kcal/mol
Surface area19910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.132, 78.217, 63.434
Angle α, β, γ (deg.)90.00, 89.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Antibody anti-dabigatran Fab1, heavy chain


Mass: 23767.596 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
#2: Antibody anti-dabigatran Fab1, light chain


Mass: 24068.959 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 366 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.93 Å3/Da / Density % sol: 58.07 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.89→39.109 Å / Num. obs: 75791 / Biso Wilson estimate: 27.77 Å2

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Processing

SoftwareName: BUSTER / Version: 2.11.2 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.89→40 Å / Cor.coef. Fo:Fc: 0.9474 / Cor.coef. Fo:Fc free: 0.9366 / SU R Cruickshank DPI: 0.121 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1966 1335 3.02 %RANDOM
Rwork0.1763 ---
obs0.1769 44143 99.57 %-
Displacement parametersBiso mean: 31.84 Å2
Baniso -1Baniso -2Baniso -3
1-6.1645 Å20 Å21.3245 Å2
2---7.2948 Å20 Å2
3---1.1303 Å2
Refine analyzeLuzzati coordinate error obs: 0.198 Å
Refinement stepCycle: LAST / Resolution: 1.89→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3368 0 48 366 3782
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083543HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.054832HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1181SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes68HARMONIC2
X-RAY DIFFRACTIONt_gen_planes528HARMONIC5
X-RAY DIFFRACTIONt_it3543HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.48
X-RAY DIFFRACTIONt_other_torsion14.36
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion471SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies13HARMONIC1
X-RAY DIFFRACTIONt_utility_distance10HARMONIC1
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4246SEMIHARMONIC4
LS refinement shellResolution: 1.89→1.94 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2271 99 3.04 %
Rwork0.2034 3156 -
all0.2041 3255 -
obs--99.57 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.9360.4427-0.27560.4662-0.28060.5534-0.01720.1422-0.1185-0.03130.0342-0.01880.0369-0.0276-0.017-0.0485-0.0085-0.0079-0.0123-0.0166-0.0486-2.559112-18.0952
20.90550.74840.05421.1821-0.07230.37980.0677-0.0444-0.00370.1277-0.01920.1239-0.0085-0.0988-0.0485-0.04650.00470.0102-0.0302-0.0082-0.0611-16.178721.2431-11.6823
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ H|2 - H|226 }H2 - 226
2X-RAY DIFFRACTION2{ L|2 - L|220 }L2 - 220

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