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- PDB-4yhl: Reversal Agent for Dabigatran -

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Basic information

Entry
Database: PDB / ID: 4yhl
TitleReversal Agent for Dabigatran
Components
  • aDabi-Fab2b heavy chain
  • aDabi-Fab2b light chain
KeywordsIMMUNE SYSTEM / Antibody / Dabigatran / Pradaxa / Antidote / Reversal Agent
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.09 Å
AuthorsSchiele, F. / Nar, H.
CitationJournal: Mabs / Year: 2015
Title: Structure-guided residence time optimization of a dabigatran reversal agent.
Authors: Schiele, F. / van Ryn, J. / Litzenburger, T. / Ritter, M. / Seeliger, D. / Nar, H.
History
DepositionFeb 27, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jan 13, 2016Provider: repository / Type: Initial release
Revision 1.1Jan 10, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: aDabi-Fab2b heavy chain
L: aDabi-Fab2b light chain


Theoretical massNumber of molelcules
Total (without water)47,7322
Polymers47,7322
Non-polymers00
Water5,873326
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-26 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)103.694, 103.694, 84.919
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number169
Space group name H-MP61

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Components

#1: Antibody aDabi-Fab2b heavy chain


Mass: 23744.479 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetinae (hamsters)
#2: Antibody aDabi-Fab2b light chain


Mass: 23987.822 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetinae (hamsters)
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 326 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.76 Å3/Da / Density % sol: 55.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 100 mM PCB buffer (pH 6) and 25% PEG 1500

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 0.91 Å
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Feb 10, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91 Å / Relative weight: 1
ReflectionResolution: 2.09→51.85 Å / Num. obs: 30655 / % possible obs: 100 % / Redundancy: 10.1 % / Biso Wilson estimate: 39.53 Å2 / Rmerge(I) obs: 0.11 / Net I/σ(I): 15.8
Reflection shellResolution: 2.09→2.16 Å / Redundancy: 10.4 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 3.4 / % possible all: 100

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata scaling
XDSdata reduction
BUSTER-TNTphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1C1E

1c1e


Resolution: 2.09→18.43 Å / Cor.coef. Fo:Fc: 0.9488 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.181 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.187 / SU Rfree Blow DPI: 0.161 / SU Rfree Cruickshank DPI: 0.16
RfactorNum. reflection% reflectionSelection details
Rfree0.2211 1542 5.04 %RANDOM
Rwork0.1813 ---
obs0.1833 30575 99.48 %-
Displacement parametersBiso mean: 40.48 Å2
Baniso -1Baniso -2Baniso -3
1-4.6822 Å20 Å20 Å2
2--4.6822 Å20 Å2
3----9.3644 Å2
Refine analyzeLuzzati coordinate error obs: 0.232 Å
Refinement stepCycle: 1 / Resolution: 2.09→18.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3330 0 0 326 3656
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0083414HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.074643HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1126SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes67HARMONIC2
X-RAY DIFFRACTIONt_gen_planes499HARMONIC5
X-RAY DIFFRACTIONt_it3414HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.37
X-RAY DIFFRACTIONt_other_torsion15.18
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion450SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4033SEMIHARMONIC4
LS refinement shellResolution: 2.09→2.16 Å / Total num. of bins used: 15
RfactorNum. reflection% reflection
Rfree0.207 142 4.95 %
Rwork0.1959 2725 -
all0.1965 2867 -
obs--99.48 %

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