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- PDB-4jn2: An Antidote for Dabigatran -

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Basic information

Entry
Database: PDB / ID: 4jn2
TitleAn Antidote for Dabigatran
Components(anti dabigatran Fab) x 2
Keywordsimmune system/inhibitor / IgG fragment binding dabigatran / dabigatran / immune system-inhibitor complex
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Chem-4CC
Function and homology information
Biological speciesMus musculus (house mouse)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.71 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 1.2Mar 11, 2015Group: Non-polymer description

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: anti dabigatran Fab
B: anti dabigatran Fab
H: anti dabigatran Fab
L: anti dabigatran Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,35314
Polymers95,6734
Non-polymers1,68010
Water23,5281306
1
A: anti dabigatran Fab
B: anti dabigatran Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6767
Polymers47,8372
Non-polymers8405
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5200 Å2
ΔGint-25 kcal/mol
Surface area19900 Å2
MethodPISA
2
H: anti dabigatran Fab
L: anti dabigatran Fab
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,6767
Polymers47,8372
Non-polymers8405
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5720 Å2
ΔGint-31 kcal/mol
Surface area19830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.161, 223.816, 157.211
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Antibody anti dabigatran Fab


Mass: 24068.959 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
#2: Antibody anti dabigatran Fab


Mass: 23767.596 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mus musculus (house mouse)
#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: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


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


Mass: 18.015 Da / Num. of mol.: 1306 / 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: 3.41 Å3/Da / Density % sol: 63.92 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.71→24.939 Å / Num. obs: 141489 / Biso Wilson estimate: 25.54 Å2

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Processing

SoftwareName: BUSTER / Version: 2.11.1 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.71→25.04 Å / Cor.coef. Fo:Fc: 0.9619 / Cor.coef. Fo:Fc free: 0.9566 / SU R Cruickshank DPI: 0.079 / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.1816 7050 5.01 %RANDOM
Rwork0.1673 ---
obs0.168 140590 99.85 %-
Displacement parametersBiso mean: 32.03 Å2
Baniso -1Baniso -2Baniso -3
1-2.6344 Å20 Å20 Å2
2---2.2361 Å20 Å2
3----0.3983 Å2
Refine analyzeLuzzati coordinate error obs: 0.209 Å
Refinement stepCycle: LAST / Resolution: 1.71→25.04 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6652 0 118 1306 8076
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0087115HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.049729HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2334SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes129HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1066HARMONIC5
X-RAY DIFFRACTIONt_it7115HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.78
X-RAY DIFFRACTIONt_other_torsion14.3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion931SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies28HARMONIC1
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact8969SEMIHARMONIC4
LS refinement shellResolution: 1.71→1.75 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2053 494 4.79 %
Rwork0.1979 9818 -
all0.1982 10312 -
obs--99.85 %
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)
12.07570.05370.22380.19530.06970.20980.0681-0.0643-0.13580.0345-0.03070.02290.00770.0289-0.0374-0.05280.0038-0.002-0.0655-0.0435-0.038-21.454227.1296-8.5337
21.8433-0.7304-0.26231.10020.58410.38-0.04-0.19160.46760.05840.0558-0.1339-0.0250.0007-0.0158-0.0866-0.0072-0.0279-0.0883-0.0930.0325-12.980541.3361-2.1545
30.5032-0.28070.30070.3119-0.27240.3691-0.0133-0.0583-0.00610.05380.0260.07480.1177-0.2011-0.01270.0126-0.01790.00630.0241-0.0027-0.0628-52.0883-2.2121-29.6958
40.4321-0.03550.04610.6083-0.33840.8017-0.00760.029-0.01790.058-0.0132-0.01390.10730.0180.0209-0.01610.00340.0002-0.018-0.0134-0.0825-39.76256.8743-21.1122
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ A|2 - A|220 }A2 - 220
2X-RAY DIFFRACTION2{ B|3 - B|226 }B3 - 226
3X-RAY DIFFRACTION3{ H|2 - H|226 }H2 - 226
4X-RAY DIFFRACTION4{ L|2 - L|220 }L2 - 220

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