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- PDB-5alc: Ticagrelor antidote candidate Fab 72 in complex with ticagrelor -

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Basic information

Entry
Database: PDB / ID: 5alc
TitleTicagrelor antidote candidate Fab 72 in complex with ticagrelor
Components
  • ANTI-TICAGRELOR FAB 72, HEAVY CHAIN
  • ANTI-TICAGRELOR FAB 72, LIGHT CHAIN
KeywordsIMMUNE SYSTEM / ANTIBODY FRAGMENT / ANTIDOTE / DRUG
Function / homologyImmunoglobulins / Immunoglobulin-like / Sandwich / Mainly Beta / Ticagrelor
Function and homology information
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsBuchanan, A. / Newton, P. / Pehrsson, S. / Inghardt, T. / Antonsson, T. / Svensson, P. / Sjogren, T. / Oster, L. / Janefeldt, A. / Sandinge, A. ...Buchanan, A. / Newton, P. / Pehrsson, S. / Inghardt, T. / Antonsson, T. / Svensson, P. / Sjogren, T. / Oster, L. / Janefeldt, A. / Sandinge, A. / Keyes, F. / Austin, M. / Spooner, J. / Penney, M. / Howells, G. / Vaughan, T. / Nylander, S.
CitationJournal: Blood / Year: 2015
Title: Structural and Functional Characterisation of a Specific Antidote for Ticagrelor.
Authors: Buchanan, A. / Newton, P. / Pehrsson, S. / Inghardt, T. / Antonsson, T. / Svensson, P. / Sjogren, T. / Oster, L. / Janefeldt, A. / Sandinge, A. / Keyes, F. / Austin, M. / Spooner, J. / ...Authors: Buchanan, A. / Newton, P. / Pehrsson, S. / Inghardt, T. / Antonsson, T. / Svensson, P. / Sjogren, T. / Oster, L. / Janefeldt, A. / Sandinge, A. / Keyes, F. / Austin, M. / Spooner, J. / Gennemark, P. / Penney, M. / Howells, G. / Vaughan, T. / Nylander, S.
History
DepositionMar 7, 2015Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 1, 2015Provider: repository / Type: Initial release
Revision 1.1Jun 10, 2015Group: Database references
Revision 1.2Jan 10, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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

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Assembly

Deposited unit
H: ANTI-TICAGRELOR FAB 72, HEAVY CHAIN
L: ANTI-TICAGRELOR FAB 72, LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)47,8233
Polymers47,3012
Non-polymers5231
Water3,783210
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3710 Å2
ΔGint-25.9 kcal/mol
Surface area18980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)41.230, 72.567, 67.765
Angle α, β, γ (deg.)90.00, 98.92, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Antibody ANTI-TICAGRELOR FAB 72, HEAVY CHAIN


Mass: 24646.473 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO-K1 / Production host: CRICETULUS GRISEUS (Chinese hamster)
#2: Antibody ANTI-TICAGRELOR FAB 72, LIGHT CHAIN


Mass: 22654.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): CHO-K1 / Production host: CRICETULUS GRISEUS (Chinese hamster)
#3: Chemical ChemComp-TIQ / Ticagrelor / Ticagrelor


Mass: 522.568 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H28F2N6O4S / Comment: medication, inhibitor*YM
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 210 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsENGINEERED ANTIBIODY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.91 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.976
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Oct 25, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.7→49.2 Å / Num. obs: 143002 / % possible obs: 97 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Biso Wilson estimate: 30.08 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 13.6
Reflection shellResolution: 1.7→1.87 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.74 / Mean I/σ(I) obs: 1.7 / % possible all: 95.3

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1AQK

1aqk


Resolution: 1.7→49.21 Å / Cor.coef. Fo:Fc: 0.9522 / Cor.coef. Fo:Fc free: 0.9363 / SU R Cruickshank DPI: 0.117 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.117 / SU Rfree Blow DPI: 0.115 / SU Rfree Cruickshank DPI: 0.116
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2367 2122 5.07 %RANDOM
Rwork0.1975 ---
obs0.1995 41864 96.35 %-
Displacement parametersBiso mean: 33.38 Å2
Baniso -1Baniso -2Baniso -3
1--3.5054 Å20 Å2-2.4352 Å2
2--1.4536 Å20 Å2
3---2.0518 Å2
Refine analyzeLuzzati coordinate error obs: 0.224 Å
Refinement stepCycle: LAST / Resolution: 1.7→49.21 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3145 0 36 210 3391
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013263HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.234458HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1041SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes61HARMONIC2
X-RAY DIFFRACTIONt_gen_planes481HARMONIC5
X-RAY DIFFRACTIONt_it3263HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.77
X-RAY DIFFRACTIONt_other_torsion18.6
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion443SEMIHARMONIC5
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_contact3819SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.2609 134 5.03 %
Rwork0.2363 2531 -
all0.2375 2665 -
obs--96.35 %

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