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- PDB-4ygv: Reversal Agent for Dabigatran -

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Basic information

Entry
Database: PDB / ID: 4ygv
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
Function and homology information
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.76 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 26, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Jun 17, 2015Provider: repository / Type: Initial release
Revision 1.1Sep 2, 2015Group: Database references
Revision 1.2Jan 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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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
F: aDabi-Fab2a heavy chain
L: aDabi-Fab2a light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,9076
Polymers95,7234
Non-polymers1842
Water14,898827
1
A: aDabi-Fab2a heavy chain
B: aDabi-Fab2a light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9543
Polymers47,8612
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3930 Å2
ΔGint-27 kcal/mol
Surface area19170 Å2
MethodPISA
2
F: aDabi-Fab2a heavy chain
L: aDabi-Fab2a light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,9543
Polymers47,8612
Non-polymers921
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3970 Å2
ΔGint-27 kcal/mol
Surface area19340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)55.933, 56.152, 81.498
Angle α, β, γ (deg.)87.38, 82.97, 65.59
Int Tables number1
Space group name H-MP1

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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: Cricetulus griseus (Chinese hamster)
#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: Cricetulus griseus (Chinese hamster)
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 827 / 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: 2.43 Å3/Da / Density % sol: 49.42 %
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: 1.76→40 Å / Num. obs: 85139 / % possible obs: 95.8 % / Redundancy: 1.8 % / Biso Wilson estimate: 19.6 Å2 / Net I/σ(I): 7.5
Reflection shellResolution: 1.76→1.81 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.445 / Mean I/σ(I) obs: 2.3 / Num. unique all: 12315 / % possible all: 95

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Processing

Software
NameVersionClassification
BUSTER2.11.2refinement
XDSdata reduction
BUSTER-TNTphasing
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3PP3

3pp3


Resolution: 1.76→40 Å / Cor.coef. Fo:Fc: 0.9406 / Cor.coef. Fo:Fc free: 0.9213 / SU R Cruickshank DPI: 0.118 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.121 / SU Rfree Blow DPI: 0.106 / SU Rfree Cruickshank DPI: 0.105
RfactorNum. reflection% reflectionSelection details
Rfree0.1982 4270 5.02 %RANDOM
Rwork0.1781 ---
obs0.1792 85139 95.8 %-
Displacement parametersBiso mean: 21.75 Å2
Baniso -1Baniso -2Baniso -3
1--0.2719 Å21.3557 Å2-4.029 Å2
2---0.2528 Å2-3.006 Å2
3---0.5246 Å2
Refine analyzeLuzzati coordinate error obs: 0.187 Å
Refinement stepCycle: LAST / Resolution: 1.76→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6701 0 12 827 7540
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0086882HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.039363HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2279SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes140HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1004HARMONIC5
X-RAY DIFFRACTIONt_it6882HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.7
X-RAY DIFFRACTIONt_other_torsion14.51
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion909SEMIHARMONIC5
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_contact8392SEMIHARMONIC4
LS refinement shellResolution: 1.76→1.81 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2237 267 4.49 %
Rwork0.2137 5675 -
all0.2141 5942 -
obs--95.8 %

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