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- PDB-4yhi: Reversal Agent for Dabigatran -

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Basic information

Entry
Database: PDB / ID: 4yhi
TitleReversal Agent for Dabigatran
Components
  • aDabi-Fab2a heavy chain
  • aDabi-Fab2a light chain
KeywordsIMMUNE SYSTEM / Antibody / Dabigatran / Pradaxa / Antidote / Reversal Agent
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-4CC
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 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
A: aDabi-Fab2a heavy chain
B: aDabi-Fab2a light chain
H: aDabi-Fab2a heavy chain
L: aDabi-Fab2a light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,6666
Polymers95,7234
Non-polymers9432
Water15,403855
1
A: aDabi-Fab2a heavy chain
B: aDabi-Fab2a light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3333
Polymers47,8612
Non-polymers4721
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3890 Å2
ΔGint-29 kcal/mol
Surface area19560 Å2
MethodPISA
2
H: aDabi-Fab2a heavy chain
L: aDabi-Fab2a light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,3333
Polymers47,8612
Non-polymers4721
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3910 Å2
ΔGint-30 kcal/mol
Surface area19530 Å2
MethodPISA
Unit cell
Length a, b, c (Å)51.806, 128.920, 60.256
Angle α, β, γ (deg.)90.00, 92.30, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody aDabi-Fab2a heavy chain


Mass: 23744.479 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetinae (hamsters)
#2: Antibody aDabi-Fab2a light chain


Mass: 24116.936 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Cricetinae (hamsters)
#3: Chemical ChemComp-4CC / N-[(2-{[(4-carbamimidoylphenyl)amino]methyl}-1-methyl-1H-benzimidazol-5-yl)carbonyl]-N-pyridin-2-yl-beta-alanine / Dabigatran


Mass: 471.511 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H25N7O3 / Comment: anticoagulant*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 855 / 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: 2.1 Å3/Da / Density % sol: 41.44 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / Details: 100 mM SPG 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: 1.9→128.92 Å / Num. obs: 61726 / % possible obs: 99.4 % / Redundancy: 3.3 % / Biso Wilson estimate: 22.76 Å2 / Rmerge(I) obs: 0.12 / Net I/σ(I): 9.6
Reflection shellResolution: 1.9→1.95 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.6 / Mean I/σ(I) obs: 2.4 / % possible all: 99.34

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Processing

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

1c1e


Resolution: 1.9→40 Å / Cor.coef. Fo:Fc: 0.9365 / Cor.coef. Fo:Fc free: 0.9142 / SU R Cruickshank DPI: 0.171 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.181 / SU Rfree Blow DPI: 0.146 / SU Rfree Cruickshank DPI: 0.144
RfactorNum. reflection% reflectionSelection details
Rfree0.2146 3116 5.05 %RANDOM
Rwork0.1811 ---
obs0.1828 61647 99.34 %-
Displacement parametersBiso mean: 23.68 Å2
Baniso -1Baniso -2Baniso -3
1--5.7269 Å20 Å22.7149 Å2
2--1.7131 Å20 Å2
3---4.0138 Å2
Refine analyzeLuzzati coordinate error obs: 0.218 Å
Refinement stepCycle: 1 / Resolution: 1.9→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6733 0 70 855 7658
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086982HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.079507HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2307SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes142HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1024HARMONIC5
X-RAY DIFFRACTIONt_it6982HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.42
X-RAY DIFFRACTIONt_other_torsion15.58
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion915SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies3HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8523SEMIHARMONIC4
LS refinement shellResolution: 1.9→1.95 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2523 218 4.8 %
Rwork0.2227 4325 -
all0.2241 4543 -
obs--99.34 %

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