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- PDB-8bo6: COAGULATION FACTOR XI PROTEASE DOMAIN IN COMPLEX WITH ACTIVE SITE... -

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Basic information

Entry
Database: PDB / ID: 8bo6
TitleCOAGULATION FACTOR XI PROTEASE DOMAIN IN COMPLEX WITH ACTIVE SITE INHIBITOR 2
ComponentsCoagulation factor XIa light chain
KeywordsBLOOD CLOTTING / S1 PROTEASE / SERINE PROTEASE / STRUCTURE-BASED DRUG DESIGN / ACTIVE SITE DIRECTED INHIBITOR / HYDROLASE
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 / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan
Similarity search - Domain/homology
CITRIC ACID / Chem-QW0 / Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.25 Å
AuthorsSchaefer, M. / Roehrig, S. / Ackerstaff, J. / Nunez, E.J. / Gericke, K.M. / Meier, K. / Tersteegen, A. / Stampfuss, J. / Ellerbrock, P. / Meibom, D. ...Schaefer, M. / Roehrig, S. / Ackerstaff, J. / Nunez, E.J. / Gericke, K.M. / Meier, K. / Tersteegen, A. / Stampfuss, J. / Ellerbrock, P. / Meibom, D. / Lang, D. / Heitmeier, S. / Hillisch, A.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: J.Med.Chem. / Year: 2023
Title: Design and Preclinical Characterization Program toward Asundexian (BAY 2433334), an Oral Factor XIa Inhibitor for the Prevention and Treatment of Thromboembolic Disorders.
Authors: Roehrig, S. / Ackerstaff, J. / Jimenez Nunez, E. / Teller, H. / Ellerbrock, P. / Meier, K. / Heitmeier, S. / Tersteegen, A. / Stampfuss, J. / Lang, D. / Schlemmer, K.H. / Schaefer, M. / ...Authors: Roehrig, S. / Ackerstaff, J. / Jimenez Nunez, E. / Teller, H. / Ellerbrock, P. / Meier, K. / Heitmeier, S. / Tersteegen, A. / Stampfuss, J. / Lang, D. / Schlemmer, K.H. / Schaefer, M. / Gericke, K.M. / Kinzel, T. / Meibom, D. / Schmidt, M. / Gerdes, C. / Follmann, M. / Hillisch, A.
History
DepositionNov 14, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 13, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 20, 2023Group: Database references / Structure summary / Category: citation / entity / entity_name_com
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _entity.pdbx_description / _entity.pdbx_ec
Revision 1.2Nov 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
AAA: Coagulation factor XIa light chain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,9127
Polymers26,8561
Non-polymers1,0566
Water4,089227
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1190 Å2
ΔGint1 kcal/mol
Surface area11270 Å2
MethodPISA
Unit cell
Length a, b, c (Å)59.120, 59.634, 67.053
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Coagulation factor XIa light chain


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: Komagataella pastoris (fungus) / References: UniProt: P03951
#2: Chemical ChemComp-QW0 / (~{E})-~{N}-[[5-(3-azanyl-1~{H}-indazol-6-yl)-4-chloranyl-1~{H}-imidazol-2-yl]methyl]-3-[5-chloranyl-2-(1,2,3,4-tetrazol-1-yl)phenyl]prop-2-enamide


Mass: 495.324 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H16Cl2N10O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#4: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 227 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.2 Å3/Da / Density % sol: 44.11 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 0.1M citrate buffer pH 4.5 and 20-30% PEG4000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 1, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.25→44.561 Å / Num. obs: 65835 / % possible obs: 99.4 % / Redundancy: 7.9 % / CC1/2: 1 / Rrim(I) all: 0.049 / Net I/σ(I): 23.09
Reflection shellResolution: 1.25→1.28 Å / Mean I/σ(I) obs: 2.75 / Num. unique obs: 4814 / CC1/2: 0.824 / Rrim(I) all: 0.825

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: in house model

Resolution: 1.25→44.561 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.973 / SU B: 1.472 / SU ML: 0.027 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.033
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1407 888 1.349 %
Rwork0.1161 64947 -
all0.116 --
obs-65835 99.413 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 20.377 Å2
Baniso -1Baniso -2Baniso -3
1-1.257 Å20 Å2-0 Å2
2---1.511 Å20 Å2
3---0.254 Å2
Refinement stepCycle: LAST / Resolution: 1.25→44.561 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1880 0 71 227 2178
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132128
X-RAY DIFFRACTIONr_bond_other_d0.0010.0151964
X-RAY DIFFRACTIONr_angle_refined_deg1.6611.6692905
X-RAY DIFFRACTIONr_angle_other_deg1.4831.5954529
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8355265
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.06321.532111
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.41915358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8611516
X-RAY DIFFRACTIONr_chiral_restr0.0890.2269
X-RAY DIFFRACTIONr_chiral_restr_other0.0390.21
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.022440
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02513
X-RAY DIFFRACTIONr_nbd_refined0.1970.2378
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1910.21830
X-RAY DIFFRACTIONr_nbtor_refined0.1720.2969
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2931
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1420.2151
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2850.220
X-RAY DIFFRACTIONr_nbd_other0.2130.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1320.224
X-RAY DIFFRACTIONr_mcbond_it1.8861.7291005
X-RAY DIFFRACTIONr_mcbond_other1.8741.7231004
X-RAY DIFFRACTIONr_mcangle_it2.42.6071271
X-RAY DIFFRACTIONr_mcangle_other2.4052.6131272
X-RAY DIFFRACTIONr_scbond_it3.3592.2191123
X-RAY DIFFRACTIONr_scbond_other3.3582.2211124
X-RAY DIFFRACTIONr_scangle_it4.0633.1431627
X-RAY DIFFRACTIONr_scangle_other4.0623.1451628
X-RAY DIFFRACTIONr_lrange_it4.52322.0292418
X-RAY DIFFRACTIONr_lrange_other4.35321.3972374
X-RAY DIFFRACTIONr_rigid_bond_restr2.55134092
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.25-1.2820.253650.2247470.2248400.8190.83299.42150.184
1.282-1.3180.251630.19746290.19847170.830.88399.470.162
1.318-1.3560.186620.16645070.16645850.9180.92699.6510.131
1.356-1.3970.174600.15343860.15344620.9170.9499.64140.119
1.397-1.4430.163580.13742350.13843060.9490.95199.69810.107
1.443-1.4940.152560.12741440.12842110.950.96199.73880.101
1.494-1.550.147540.11439640.11440250.9660.96999.82610.09
1.55-1.6130.164530.10538410.10639060.970.97499.69280.084
1.613-1.6850.143500.136970.137540.9750.97899.81350.082
1.685-1.7670.124480.0935180.0935720.9770.98399.8320.075
1.767-1.8630.113470.09133790.09134310.9830.98399.85430.079
1.863-1.9750.12430.09231710.09232210.9770.98499.78270.083
1.975-2.1110.115410.0929980.0930440.9820.98599.83570.086
2.111-2.280.111380.09328230.09328620.9840.98599.96510.092
2.28-2.4970.13360.09825990.09826360.9770.98599.96210.1
2.497-2.7910.123320.10223590.10223910.9830.9851000.11
2.791-3.220.127290.11120940.11121280.9820.98499.7650.124
3.22-3.9390.136240.11417860.11518290.9810.98698.96120.135
3.939-5.5490.131180.12813320.12814420.980.98193.620.167
5.549-44.5610.251110.2217380.2218620.8990.94186.8910.273

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