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- PDB-3sos: Benzothiazinone inhibitor in complex with FXIa -

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Basic information

Entry
Database: PDB / ID: 3sos
TitleBenzothiazinone inhibitor in complex with FXIa
ComponentsCoagulation factor XI
KeywordsHydrolase/Hydrolase Inhibitor / hydrolase / serine protease / coagulation factor / Hydrolase-Hydrolase Inhibitor 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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. ...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 / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, histidine active site. / 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 / Peptidase S1, PA clan / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
N-[(2S)-1-({2-[5-CHLORO-2-(1H-TETRAZOL-1-YL)PHENYL]ETHYL}AMINO)-1-OXO-3-PHENYLPROPAN-2-YL]-3-OXO-3,4-DIHYDRO-2H-1,4-BENZOTHIAZINE-7-CARBOXAMIDE / CITRIC ACID / Chem-O61 / Coagulation factor XI
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.58 Å
AuthorsFradera, X. / Kazemier, B. / Oubrie, A.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2012
Title: High-resolution crystal structures of factor XIa coagulation factor in complex with nonbasic high-affinity synthetic inhibitors.
Authors: Fradera, X. / Kazemier, B. / Carswell, E. / Cooke, A. / Oubrie, A. / Hamilton, W. / Dempster, M. / Krapp, S. / Nagel, S. / Jestel, A.
History
DepositionJun 30, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 11, 2012Provider: repository / Type: Initial release
Revision 1.1Dec 12, 2012Group: Other
Revision 1.2Jan 23, 2013Group: Database references
Revision 1.3Apr 3, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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

Downloads & links

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Assembly

Deposited unit
A: Coagulation factor XI
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,7334
Polymers26,8561
Non-polymers8763
Water1,47782
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)59.114, 59.548, 66.755
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Coagulation factor XI / FXI / Plasma thromboplastin antecedent / PTA / Coagulation factor XIa heavy chain / Coagulation ...FXI / Plasma thromboplastin antecedent / PTA / Coagulation factor XIa heavy chain / 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, coagulation factor XIa
#2: Chemical ChemComp-CIT / CITRIC ACID


Mass: 192.124 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#4: Chemical ChemComp-O61 / N-[(2S)-1-({2-[5-chloro-2-(1H-tetrazol-1-yl)phenyl]ethyl}amino)-1-oxo-3-phenylpropan-2-yl]-3-oxo-3,4-dihydro-2H-1,4-benzothiazine-7-carboxamide


Type: peptide-like, Peptide-like / Class: Enzyme inhibitor / Mass: 562.043 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C27H24ClN7O3S
References: N-[(2S)-1-({2-[5-CHLORO-2-(1H-TETRAZOL-1-YL)PHENYL]ETHYL}AMINO)-1-OXO-3-PHENYLPROPAN-2-YL]-3-OXO-3,4-DIHYDRO-2H-1,4-BENZOTHIAZINE-7-CARBOXAMIDE
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 82 / 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: 2.19 Å3/Da / Density % sol: 43.77 %
Crystal growTemperature: 293 K
Details: Co-crystallization by adding seeds to the crystal drops using a Hampton seed hair. crystal. solutin: 0.1 M citrate pH 4.5 - 5.25, 22 - 24 % PEG4000. cryoprotectant: 75 % mother liquor + 25 % ...Details: Co-crystallization by adding seeds to the crystal drops using a Hampton seed hair. crystal. solutin: 0.1 M citrate pH 4.5 - 5.25, 22 - 24 % PEG4000. cryoprotectant: 75 % mother liquor + 25 % Glycerol, temperature 293K

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Data collection

Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF
DetectorDetector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.73→44.46 Å / Num. obs: 7446 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
CrystalCleardata collection
REFMAC5.6.0117refinement
d*TREKdata reduction
d*TREKdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: proprietary FXIa structure

Resolution: 2.58→44.46 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.904 / SU B: 12.052 / SU ML: 0.264 / Cross valid method: THROUGHOUT / ESU R Free: 0.384 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27814 362 4.6 %RANDOM
Rwork0.19904 ---
obs0.20278 7446 99.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.253 Å2
Baniso -1Baniso -2Baniso -3
1-2.09 Å20 Å20 Å2
2---1.24 Å20 Å2
3----0.86 Å2
Refinement stepCycle: LAST / Resolution: 2.58→44.46 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1875 0 60 82 2017
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.022036
X-RAY DIFFRACTIONr_bond_other_d0.0010.021391
X-RAY DIFFRACTIONr_angle_refined_deg1.4141.9632773
X-RAY DIFFRACTIONr_angle_other_deg0.8523.0053375
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3145249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40423.80492
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.89615346
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7341513
X-RAY DIFFRACTIONr_chiral_restr0.080.2291
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.022259
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02423
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.1860.2909
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2080.2105
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2790.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2530.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1590.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2481.51530
X-RAY DIFFRACTIONr_mcbond_other0.21.5495
X-RAY DIFFRACTIONr_mcangle_it1.53821930
X-RAY DIFFRACTIONr_scbond_it2.28631024
X-RAY DIFFRACTIONr_scangle_it3.3414.5836
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.58→2.647 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.501 24 -
Rwork0.309 465 -
obs--100 %

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