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- PDB-5alb: Ticagrelor antidote candidate MEDI2452 in complex with ticagrelor -

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Basic information

Entry
Database: PDB / ID: 5alb
TitleTicagrelor antidote candidate MEDI2452 in complex with ticagrelor
Components
  • MEDI2452 HEAVY CHAIN
  • MEDI2452 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: 2.16 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
Revision 1.3Nov 20, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
H: MEDI2452 HEAVY CHAIN
L: MEDI2452 LIGHT CHAIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0143
Polymers47,4922
Non-polymers5231
Water1,76598
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3810 Å2
ΔGint-26.9 kcal/mol
Surface area19620 Å2
MethodPISA
Unit cell
Length a, b, c (Å)69.310, 173.490, 42.580
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Antibody MEDI2452 HEAVY CHAIN


Mass: 24705.516 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 MEDI2452 LIGHT CHAIN


Mass: 22786.250 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


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


Mass: 18.015 Da / Num. of mol.: 98 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsENGINEERED ANTIBODY

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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: 2.7 Å3/Da / Density % sol: 54.36 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.972
DetectorType: DECTRIS PILATUS / Detector: PIXEL / Date: Jun 13, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.972 Å / Relative weight: 1
ReflectionResolution: 1.98→44.4 Å / Num. obs: 36570 / % possible obs: 99.4 % / Observed criterion σ(I): 2 / Redundancy: 6.4 % / Biso Wilson estimate: 46.98 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.7
Reflection shellResolution: 1.98→2.05 Å / Redundancy: 6.4 % / Rmerge(I) obs: 1.31 / Mean I/σ(I) obs: 1.1 / % possible all: 94.9

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Processing

Software
NameVersionClassification
BUSTER2.11.6refinement
XDSdata reduction
Aimlessdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1AQK

1aqk


Resolution: 2.16→41 Å / Cor.coef. Fo:Fc: 0.9187 / Cor.coef. Fo:Fc free: 0.8816 / SU R Cruickshank DPI: 0.22 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.223 / SU Rfree Blow DPI: 0.192 / SU Rfree Cruickshank DPI: 0.193
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2592 1391 4.89 %RANDOM
Rwork0.214 ---
obs0.2162 28427 99.86 %-
Displacement parametersBiso mean: 44.21 Å2
Baniso -1Baniso -2Baniso -3
1--0.9428 Å20 Å20 Å2
2--6.4859 Å20 Å2
3----5.5431 Å2
Refine analyzeLuzzati coordinate error obs: 0.305 Å
Refinement stepCycle: LAST / Resolution: 2.16→41 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3248 0 36 98 3382
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.013375HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.254616HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1071SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes62HARMONIC2
X-RAY DIFFRACTIONt_gen_planes501HARMONIC5
X-RAY DIFFRACTIONt_it3375HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.55
X-RAY DIFFRACTIONt_other_torsion20.43
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion454SEMIHARMONIC5
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_contact3720SEMIHARMONIC4
LS refinement shellResolution: 2.16→2.24 Å / Total num. of bins used: 14
RfactorNum. reflection% reflection
Rfree0.2282 132 4.44 %
Rwork0.2235 2840 -
all0.2237 2972 -
obs--99.86 %

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