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- PDB-6hhc: Allosteric Inhibition as a new mode of Action for BAY 1213790, a ... -

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Basic information

Entry
Database: PDB / ID: 6hhc
TitleAllosteric Inhibition as a new mode of Action for BAY 1213790, a Neutralizing Antibody Targeting the Activated form of Coagulation Factor XI
Components
  • Coagulation factor XI
  • FXIA ANTIBODY FAB HEAVY CHAIN
  • FXIA ANTIBODY FAB LIGHT CHAIN
KeywordsBLOOD CLOTTING / FXIA ANTIBODY FAB / BLOOD CLOTTING-IMMUNE COMPLEX
Function / homology
Function and homology information


coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space ...coagulation factor XIa / serine-type aminopeptidase activity / Defective F9 activation / positive regulation of fibrinolysis / plasminogen activation / Intrinsic Pathway of Fibrin Clot Formation / blood coagulation / heparin binding / serine-type endopeptidase activity / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / plasma membrane
Similarity search - Function
Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family ...Apple domain. / Apple domain / APPLE domain / PAN/Apple domain profile. / PAN domain / PAN/Apple domain / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / Trypsin-like serine proteases / Thrombin, subunit H / Peptidase S1, PA clan, chymotrypsin-like fold / Immunoglobulins / Peptidase S1, PA clan / Beta Barrel / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.7 Å
AuthorsSchaefer, M. / Buchmueller, A. / Dittmer, F. / Strassburger, J. / Wilmen, A.
CitationJournal: J.Mol.Biol. / Year: 2019
Title: Allosteric Inhibition as a New Mode of Action for BAY 1213790, a Neutralizing Antibody Targeting the Activated Form of Coagulation Factor XI.
Authors: Schaefer, M. / Buchmueller, A. / Dittmer, F. / Strassburger, J. / Wilmen, A.
History
DepositionAug 27, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 11, 2019Provider: repository / Type: Initial release
Revision 1.1Nov 6, 2019Group: Data collection / Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID
Revision 1.2Dec 25, 2019Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
Revision 1.3Jan 17, 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 1.4Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
L: FXIA ANTIBODY FAB LIGHT CHAIN
H: FXIA ANTIBODY FAB HEAVY CHAIN
A: Coagulation factor XI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,6557
Polymers74,2893
Non-polymers3664
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5900 Å2
ΔGint-69 kcal/mol
Surface area28670 Å2
MethodPISA
Unit cell
Length a, b, c (Å)61.941, 70.679, 185.893
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21221

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Components

#1: Antibody FXIA ANTIBODY FAB LIGHT CHAIN


Mass: 23496.895 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#2: Antibody FXIA ANTIBODY FAB HEAVY CHAIN


Mass: 23935.719 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Homo sapiens (human)
#3: Protein Coagulation factor XI / FXI / Plasma thromboplastin antecedent / PTA


Mass: 26856.496 Da / Num. of mol.: 1 / Mutation: C500S
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: F11 / Production host: Homo sapiens (human) / References: UniProt: P03951, coagulation factor XIa
#4: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-DMS / DIMETHYL SULFOXIDE


Mass: 78.133 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6OS / Comment: DMSO, precipitant*YM
Has protein modificationY

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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: 2.74 Å3/Da / Density % sol: 55.09 %
Crystal growTemperature: 293 K / Method: evaporation / pH: 7.5 / Details: 20 mM Tris-HCl pH 7.5,75 mM NaCl

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91832 Å
DetectorType: MAR CCD 130 mm / Detector: CCD / Date: May 15, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91832 Å / Relative weight: 1
ReflectionResolution: 2.7→99 Å / Num. obs: 23127 / % possible obs: 99.8 % / Redundancy: 4.2 % / Net I/σ(I): 9.41
Reflection shellResolution: 2.7→2.86 Å

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassification
XDSdata reduction
SCALAdata scaling
MOLREPphasing
BALBESphasing
REFMAC5.8.0189refinement
PDB_EXTRACT3.24data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3GJE

3gje


Resolution: 2.7→92.95 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.815 / SU B: 36.909 / SU ML: 0.337 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 1.077 / ESU R Free: 0.415
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.3144 1182 5.1 %RANDOM
Rwork0.2274 ---
obs0.2317 21948 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 116.08 Å2 / Biso mean: 38.936 Å2 / Biso min: 16.36 Å2
Baniso -1Baniso -2Baniso -3
1--0.67 Å2-0 Å2-0 Å2
2---2.68 Å20 Å2
3---3.35 Å2
Refinement stepCycle: final / Resolution: 2.7→92.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5042 0 19 0 5061
Biso mean--37.99 --
Num. residues----656
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0195181
X-RAY DIFFRACTIONr_bond_other_d0.0020.024622
X-RAY DIFFRACTIONr_angle_refined_deg2.1711.9467038
X-RAY DIFFRACTIONr_angle_other_deg1.153310781
X-RAY DIFFRACTIONr_dihedral_angle_1_deg9.2985651
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.59924.393214
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.67115840
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.0941522
X-RAY DIFFRACTIONr_chiral_restr0.1150.2779
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.0215740
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021034
LS refinement shellResolution: 2.698→2.768 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.437 69 -
Rwork0.317 1522 -
all-1591 -
obs--96.07 %
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)
10.7698-0.3512-0.08031.5966-0.81190.5738-0.2058-0.0114-0.2302-0.2160.10070.07120.1222-0.08710.10510.260.00140.03380.2367-0.00590.2-21.6857-31.889337.1
20.3932-0.173-0.1861.6023-0.1110.1203-0.1411-0.1095-0.00750.10410.1419-0.01560.02750.0557-0.00080.21150.05030.020.35580.02120.1726-17.0881-17.262448.1852
30.4946-0.05410.45165.4771-2.93361.9472-0.1686-0.32220.1224-1.37020.0404-0.03860.5157-0.26780.12820.6733-0.0126-0.04440.2667-0.07560.0307-13.477515.126111.9274
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1L3 - 215
2X-RAY DIFFRACTION2H1 - 221
3X-RAY DIFFRACTION3A388 - 623

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